commit/galaxy-central: greg: Add the ability to view an SVG image of a workflow contained in a tool shed repository installed into a Galaxy instance. This feature is the same as the feature that has been available in the tool shed for some time.

27 Dec 2012

1 new commit in galaxy-central:


https://bitbucket.org/galaxy/galaxy-central/changeset/7073d786cad0/
changeset:   7073d786cad0
user:        greg
date:        2012-12-27 22:00:16
summary:     Add the ability to view an SVG image of a workflow contained in a tool shed repository installed into a Galaxy instance.  This feature is the same as the feature that has been available in the tool shed for some time.
affected #:  14 files

diff -r 875ac898df00fd919b6b24f58562fadbf03dc5e1 -r 7073d786cad0f0d251d4ea9b2c42171f698cf953 lib/galaxy/util/shed_util_common.py

--- a/lib/galaxy/util/shed_util_common.py
+++ b/lib/galaxy/util/shed_util_common.py
@@ -1,14 +1,14 @@
 import os, shutil, tempfile, logging, string, threading, urllib2
 from galaxy import util
 from galaxy.tools import parameters
-from galaxy.util import inflector
-from galaxy.util import json
+from galaxy.util import inflector, json
 from galaxy.web import url_for
 from galaxy.web.form_builder import SelectField
 from galaxy.webapps.community.util import container_util
 from galaxy.datatypes import checkers
 from galaxy.model.orm import and_
 from galaxy.tools.parameters import dynamic_options
+from galaxy.tool_shed import encoding_util
 
 from galaxy import eggs
 import pkg_resources
@@ -176,7 +176,12 @@
             containers_dict[ 'valid_tools' ] = valid_tools_root_folder
         # Workflows container.
         if workflows:
-            folder_id, workflows_root_folder = container_util.build_workflows_folder( trans, folder_id, workflows, repository_metadata, label='Workflows' )
+            folder_id, workflows_root_folder = container_util.build_workflows_folder( trans=trans,
+                                                                                      folder_id=folder_id,
+                                                                                      workflows=workflows,
+                                                                                      repository_metadata_id=None,
+                                                                                      repository_id=repository_id,
+                                                                                      label='Workflows' )
             containers_dict[ 'workflows' ] = workflows_root_folder
     except Exception, e:
         log.debug( "Exception in build_repository_containers_for_galaxy: %s" % str( e ) )
@@ -252,7 +257,12 @@
             # Workflows container.
             if metadata and 'workflows' in metadata:
                 workflows = metadata[ 'workflows' ]
-                folder_id, workflows_root_folder = container_util.build_workflows_folder( trans, folder_id, workflows, repository_metadata, label='Workflows' )
+                folder_id, workflows_root_folder = container_util.build_workflows_folder( trans=trans,
+                                                                                          folder_id=folder_id,
+                                                                                          workflows=workflows,
+                                                                                          repository_metadata_id=repository_metadata.id,
+                                                                                          repository_id=None,
+                                                                                          label='Workflows' )
                 containers_dict[ 'workflows' ] = workflows_root_folder
         except Exception, e:
             log.debug( "Exception in build_repository_containers_for_tool_shed: %s" % str( e ) )
@@ -400,6 +410,25 @@
                             # tag for any tool in the repository.
                             break
     return can_generate_dependency_metadata
+def can_use_tool_config_disk_file( trans, repository, repo, file_path, changeset_revision ):
+    """
+    Determine if repository's tool config file on disk can be used.  This method is restricted to tool config files since, with the
+    exception of tool config files, multiple files with the same name will likely be in various directories in the repository and we're
+    comparing file names only (not relative paths).
+    """
+    if not file_path or not os.path.exists( file_path ):
+        # The file no longer exists on disk, so it must have been deleted at some previous point in the change log.
+        return False
+    if changeset_revision == repository.tip( trans.app ):
+        return True
+    file_name = strip_path( file_path )
+    latest_version_of_file = get_latest_tool_config_revision_from_repository_manifest( repo, file_name, changeset_revision )
+    can_use_disk_file = filecmp.cmp( file_path, latest_version_of_file )
+    try:
+        os.unlink( latest_version_of_file )
+    except:
+        pass
+    return can_use_disk_file
 def check_tool_input_params( app, repo_dir, tool_config_name, tool, sample_files ):
     """
     Check all of the tool's input parameters, looking for any that are dynamically generated using external data files to make 
@@ -1339,6 +1368,16 @@
     else:
         metadata_dict[ 'workflows' ] = [ ( relative_path, exported_workflow_dict ) ]
     return metadata_dict
+def get_absolute_path_to_file_in_repository( repo_files_dir, file_name ):
+    """Return the absolute path to a specified disk file containe in a repository."""
+    stripped_file_name = strip_path( file_name )
+    file_path = None
+    for root, dirs, files in os.walk( repo_files_dir ):
+        if root.find( '.hg' ) < 0:
+            for name in files:
+                if name == stripped_file_name:
+                    return os.path.abspath( os.path.join( root, name ) )
+    return file_path
 def get_changectx_for_changeset( repo, changeset_revision, **kwd ):
     """Retrieve a specified changectx from a repository"""
     for changeset in repo.changelog:
@@ -1487,14 +1526,14 @@
         repository_clone_url = os.path.join( tool_shed_url, 'repos', owner, name )
         ctx_rev = get_ctx_rev( tool_shed_url, name, owner, installed_changeset_revision )
         print "Adding new row (or updating an existing row) for repository '%s' in the tool_shed_repository table." % name
-        repository = create_or_update_tool_shed_repository( app=self.app,
+        repository = create_or_update_tool_shed_repository( app=trans.app,
                                                             name=name,
                                                             description=None,
                                                             installed_changeset_revision=changeset_revision,
                                                             ctx_rev=ctx_rev,
                                                             repository_clone_url=repository_clone_url,
                                                             metadata_dict={},
-                                                            status=self.app.model.ToolShedRepository.installation_status.NEW,
+                                                            status=trans.model.ToolShedRepository.installation_status.NEW,
                                                             current_changeset_revision=None,
                                                             owner=sowner,
                                                             dist_to_shed=False )
@@ -1712,6 +1751,9 @@
     elif all_metadata_records:
         return all_metadata_records[ 0 ]
     return None
+def get_repository_metadata_by_id( trans, id ):
+    """Get repository metadata from the database"""
+    return trans.sa_session.query( trans.model.RepositoryMetadata ).get( trans.security.decode_id( id ) )
 def get_repository_metadata_by_repository_id_changset_revision( trans, id, changeset_revision ):
     """Get a specified metadata record for a specified repository."""
     return trans.sa_session.query( trans.model.RepositoryMetadata ) \
@@ -1822,6 +1864,10 @@
                 tool_path = shed_tool_conf_dict[ 'tool_path' ]
                 break
     return tool_path
+def get_tool_shed_repository_by_id( trans, repository_id ):
+    return trans.sa_session.query( trans.model.ToolShedRepository ) \
+                           .filter( trans.model.ToolShedRepository.table.c.id == trans.security.decode_id( repository_id ) ) \
+                           .first()
 def get_tool_shed_repository_by_shed_name_owner_changeset_revision( app, tool_shed, name, owner, changeset_revision ):
     # This method is used only in Galaxy, not the tool shed.
     sa_session = app.model.context.current
@@ -2110,6 +2156,46 @@
     description = repository_dependencies_dict.get( 'description', None )
     all_repository_dependencies[ 'description' ] = description
     return all_repository_dependencies
+def load_tool_from_changeset_revision( trans, repository_id, changeset_revision, tool_config_filename ):
+    """
+    Return a loaded tool whose tool config file name (e.g., filtering.xml) is the value of tool_config_filename.  The value of changeset_revision
+    is a valid (downloadable) changset revision.  The tool config will be located in the repository manifest between the received valid changeset
+    revision and the first changeset revision in the repository, searching backwards.
+    """
+    original_tool_data_path = trans.app.config.tool_data_path
+    repository = get_repository_in_tool_shed( trans, repository_id )
+    repo_files_dir = repository.repo_path( trans.app )
+    repo = hg.repository( get_configured_ui(), repo_files_dir )
+    message = ''
+    tool = None
+    can_use_disk_file = False
+    tool_config_filepath = get_absolute_path_to_file_in_repository( repo_files_dir, tool_config_filename )
+    work_dir = tempfile.mkdtemp()
+    can_use_disk_file = can_use_tool_config_disk_file( trans, repository, repo, tool_config_filepath, changeset_revision )
+    if can_use_disk_file:
+        trans.app.config.tool_data_path = work_dir
+        tool, valid, message, sample_files = handle_sample_files_and_load_tool_from_disk( trans, repo_files_dir, tool_config_filepath, work_dir )
+        if tool is not None:
+            invalid_files_and_errors_tups = check_tool_input_params( trans.app,
+                                                                     repo_files_dir,
+                                                                     tool_config_filename,
+                                                                     tool,
+                                                                     sample_files )
+            if invalid_files_and_errors_tups:
+                message2 = generate_message_for_invalid_tools( trans,
+                                                               invalid_files_and_errors_tups,
+                                                               repository,
+                                                               metadata_dict=None,
+                                                               as_html=True,
+                                                               displaying_invalid_tool=True )
+                message = concat_messages( message, message2 )
+    else:
+        tool, message, sample_files = handle_sample_files_and_load_tool_from_tmp_config( trans, repo, changeset_revision, tool_config_filename, work_dir )
+    remove_dir( work_dir )
+    trans.app.config.tool_data_path = original_tool_data_path
+    # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file.
+    reset_tool_data_tables( trans.app )
+    return repository, tool, message
 def load_tool_from_config( app, full_path ):
     try:
         tool = app.toolbox.load_tool( full_path )


diff -r 875ac898df00fd919b6b24f58562fadbf03dc5e1 -r 7073d786cad0f0d251d4ea9b2c42171f698cf953 lib/galaxy/webapps/community/controllers/admin.py
--- a/lib/galaxy/webapps/community/controllers/admin.py
+++ b/lib/galaxy/webapps/community/controllers/admin.py
@@ -533,7 +533,7 @@
                 # The received id is a RepositoryMetadata object id, so we need to get the
                 # associated Repository and redirect to view_or_manage_repository with the
                 # changeset_revision.
-                repository_metadata = common.get_repository_metadata_by_id( trans, kwd[ 'id' ] )
+                repository_metadata = suc.get_repository_metadata_by_id( trans, kwd[ 'id' ] )
                 repository = repository_metadata.repository
                 kwd[ 'id' ] = trans.security.encode_id( repository.id )
                 kwd[ 'changeset_revision' ] = repository_metadata.changeset_revision
@@ -615,7 +615,7 @@
             ids = util.listify( id )
             count = 0
             for repository_metadata_id in ids:
-                repository_metadata = common.get_repository_metadata_by_id( trans, repository_metadata_id )
+                repository_metadata = suc.get_repository_metadata_by_id( trans, repository_metadata_id )
                 trans.sa_session.delete( repository_metadata )
                 trans.sa_session.flush()
                 count += 1


diff -r 875ac898df00fd919b6b24f58562fadbf03dc5e1 -r 7073d786cad0f0d251d4ea9b2c42171f698cf953 lib/galaxy/webapps/community/controllers/common.py
--- a/lib/galaxy/webapps/community/controllers/common.py
+++ b/lib/galaxy/webapps/community/controllers/common.py
@@ -113,25 +113,6 @@
         repository_metadata.tool_versions = tool_versions_dict
         trans.sa_session.add( repository_metadata )
         trans.sa_session.flush()
-def can_use_tool_config_disk_file( trans, repository, repo, file_path, changeset_revision ):
-    """
-    Determine if repository's tool config file on disk can be used.  This method is restricted to tool config files since, with the
-    exception of tool config files, multiple files with the same name will likely be in various directories in the repository and we're
-    comparing file names only (not relative paths).
-    """
-    if not file_path or not os.path.exists( file_path ):
-        # The file no longer exists on disk, so it must have been deleted at some previous point in the change log.
-        return False
-    if changeset_revision == repository.tip( trans.app ):
-        return True
-    file_name = suc.strip_path( file_path )
-    latest_version_of_file = get_latest_tool_config_revision_from_repository_manifest( repo, file_name, changeset_revision )
-    can_use_disk_file = filecmp.cmp( file_path, latest_version_of_file )
-    try:
-        os.unlink( latest_version_of_file )
-    except:
-        pass
-    return can_use_disk_file
 def changeset_is_malicious( trans, id, changeset_revision, **kwd ):
     """Check the malicious flag in repository metadata for a specified change set"""
     repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, id, changeset_revision )
@@ -155,15 +136,6 @@
             if user_email in admin_users:
                 return True
     return False
-def get_absolute_path_to_file_in_repository( repo_files_dir, file_name ):
-    stripped_file_name = suc.strip_path( file_name )
-    file_path = None
-    for root, dirs, files in os.walk( repo_files_dir ):
-        if root.find( '.hg' ) < 0:
-            for name in files:
-                if name == stripped_file_name:
-                    return os.path.abspath( os.path.join( root, name ) )
-    return file_path
 def get_category( trans, id ):
     """Get a category from the database"""
     return trans.sa_session.query( trans.model.Category ).get( trans.security.decode_id( id ) )
@@ -249,9 +221,6 @@
 def get_repository_by_name( trans, name ):
     """Get a repository from the database via name"""
     return trans.sa_session.query( trans.model.Repository ).filter_by( name=name ).one()
-def get_repository_metadata_by_id( trans, id ):
-    """Get repository metadata from the database"""
-    return trans.sa_session.query( trans.model.RepositoryMetadata ).get( trans.security.decode_id( id ) )
 def get_repository_metadata_revisions_for_review( repository, reviewed=True ):
     repository_metadata_revisions = []
     metadata_changeset_revision_hashes = []
@@ -425,46 +394,6 @@
         if previous_changeset_revision in reviewed_revision_hashes:
             return True
     return False
-def load_tool_from_changeset_revision( trans, repository_id, changeset_revision, tool_config_filename ):
-    """
-    Return a loaded tool whose tool config file name (e.g., filtering.xml) is the value of tool_config_filename.  The value of changeset_revision
-    is a valid (downloadable) changset revision.  The tool config will be located in the repository manifest between the received valid changeset
-    revision and the first changeset revision in the repository, searching backwards.
-    """
-    original_tool_data_path = trans.app.config.tool_data_path
-    repository = suc.get_repository_in_tool_shed( trans, repository_id )
-    repo_files_dir = repository.repo_path( trans.app )
-    repo = hg.repository( suc.get_configured_ui(), repo_files_dir )
-    message = ''
-    tool = None
-    can_use_disk_file = False
-    tool_config_filepath = get_absolute_path_to_file_in_repository( repo_files_dir, tool_config_filename )
-    work_dir = tempfile.mkdtemp()
-    can_use_disk_file = can_use_tool_config_disk_file( trans, repository, repo, tool_config_filepath, changeset_revision )
-    if can_use_disk_file:
-        trans.app.config.tool_data_path = work_dir
-        tool, valid, message, sample_files = suc.handle_sample_files_and_load_tool_from_disk( trans, repo_files_dir, tool_config_filepath, work_dir )
-        if tool is not None:
-            invalid_files_and_errors_tups = suc.check_tool_input_params( trans.app,
-                                                                         repo_files_dir,
-                                                                         tool_config_filename,
-                                                                         tool,
-                                                                         sample_files )
-            if invalid_files_and_errors_tups:
-                message2 = suc.generate_message_for_invalid_tools( trans,
-                                                                   invalid_files_and_errors_tups,
-                                                                   repository,
-                                                                   metadata_dict=None,
-                                                                   as_html=True,
-                                                                   displaying_invalid_tool=True )
-                message = suc.concat_messages( message, message2 )
-    else:
-        tool, message, sample_files = suc.handle_sample_files_and_load_tool_from_tmp_config( trans, repo, changeset_revision, tool_config_filename, work_dir )
-    suc.remove_dir( work_dir )
-    trans.app.config.tool_data_path = original_tool_data_path
-    # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file.
-    suc.reset_tool_data_tables( trans.app )
-    return repository, tool, message
 def new_repository_dependency_metadata_required( trans, repository, metadata_dict ):
     """
     Compare the last saved metadata for each repository dependency in the repository with the new 


diff -r 875ac898df00fd919b6b24f58562fadbf03dc5e1 -r 7073d786cad0f0d251d4ea9b2c42171f698cf953 lib/galaxy/webapps/community/controllers/repository.py
--- a/lib/galaxy/webapps/community/controllers/repository.py
+++ b/lib/galaxy/webapps/community/controllers/repository.py
@@ -1,18 +1,20 @@
-import os, logging, tempfile, shutil, ConfigParser
+import os, logging, re, tempfile, shutil, ConfigParser
 from time import gmtime, strftime
 from datetime import date, datetime
-from galaxy import util
+from galaxy import util, web
 from galaxy.util.odict import odict
-from galaxy.web.base.controller import *
-from galaxy.web.form_builder import CheckboxField
+from galaxy.web.base.controller import BaseUIController
+from galaxy.web.form_builder import CheckboxField, SelectField, build_select_field
 from galaxy.webapps.community import model
 from galaxy.webapps.community.model import directory_hash_id
-from galaxy.web.framework.helpers import time_ago, iff, grids
-from galaxy.util.json import from_json_string, to_json_string
-from galaxy.model.orm import and_
+from galaxy.web.framework.helpers import grids
+from galaxy.util import json
+from galaxy.model.orm import and_, or_
 import galaxy.util.shed_util_common as suc
 from galaxy.tool_shed import encoding_util
+from galaxy.webapps.community.util import workflow_util
 import common
+import galaxy.tools
 
 from galaxy import eggs
 eggs.require('mercurial')
@@ -157,7 +159,7 @@
                                        model.User.table.c.email == column_filter ) )
     class EmailAlertsColumn( grids.TextColumn ):
         def get_value( self, trans, grid, repository ):
-            if trans.user and repository.email_alerts and trans.user.email in from_json_string( repository.email_alerts ):
+            if trans.user and repository.email_alerts and trans.user.email in json.from_json_string( repository.email_alerts ):
                 return 'yes'
             return ''
     class DeprecatedColumn( grids.TextColumn ):
@@ -833,7 +835,7 @@
             # Start building up the url to redirect back to the calling Galaxy instance.            
             url = suc.url_join( galaxy_url,
                                 'admin_toolshed/update_to_changeset_revision?tool_shed_url=%s&name=%s&owner=%s&changeset_revision=%s&latest_changeset_revision=' % \
-                                ( url_for( '/', qualified=True ), repository.name, repository.user.username, changeset_revision ) )
+                                ( web.url_for( '/', qualified=True ), repository.name, repository.user.username, changeset_revision ) )
         if changeset_revision == repository.tip( trans.app ):
             # If changeset_revision is the repository tip, there are no additional updates.
             if from_update_manager:
@@ -1020,7 +1022,7 @@
         params = util.Params( kwd )
         message = util.restore_text( params.get( 'message', ''  ) )
         status = params.get( 'status', 'done' )
-        repository, tool, message = common.load_tool_from_changeset_revision( trans, repository_id, changeset_revision, tool_config )
+        repository, tool, message = suc.load_tool_from_changeset_revision( trans, repository_id, changeset_revision, tool_config )
         if message:
             status = 'error'
         tool_state = self.__new_state( trans )
@@ -1087,7 +1089,7 @@
                 is_admin = trans.user_is_admin()
                 if operation == "view_or_manage_repository":
                     # The received id is a RepositoryMetadata id, so we have to get the repository id.
-                    repository_metadata = common.get_repository_metadata_by_id( trans, item_id )
+                    repository_metadata = suc.get_repository_metadata_by_id( trans, item_id )
                     repository_id = trans.security.encode_id( repository_metadata.repository.id )
                     repository = suc.get_repository_in_tool_shed( trans, repository_id )
                     kwd[ 'id' ] = repository_id
@@ -1104,7 +1106,7 @@
                     encoded_repository_ids = []
                     changeset_revisions = []
                     for repository_metadata_id in util.listify( item_id ):
-                        repository_metadata = common.get_repository_metadata_by_id( trans, repository_metadata_id )
+                        repository_metadata = suc.get_repository_metadata_by_id( trans, repository_metadata_id )
                         encoded_repository_ids.append( trans.security.encode_id( repository_metadata.repository.id ) )
                         changeset_revisions.append( repository_metadata.changeset_revision )
                     new_kwd[ 'repository_ids' ] = encoded_repository_ids
@@ -1172,7 +1174,7 @@
                 is_admin = trans.user_is_admin()
                 if operation == "view_or_manage_repository":
                     # The received id is a RepositoryMetadata id, so we have to get the repository id.
-                    repository_metadata = common.get_repository_metadata_by_id( trans, item_id )
+                    repository_metadata = suc.get_repository_metadata_by_id( trans, item_id )
                     repository_id = trans.security.encode_id( repository_metadata.repository.id )
                     repository = suc.get_repository_in_tool_shed( trans, repository_id )
                     kwd[ 'id' ] = repository_id
@@ -1189,7 +1191,7 @@
                     encoded_repository_ids = []
                     changeset_revisions = []
                     for repository_metadata_id in util.listify( item_id ):
-                        repository_metadata = common.get_repository_metadata_by_id( trans, item_id )
+                        repository_metadata = suc.get_repository_metadata_by_id( trans, item_id )
                         encoded_repository_ids.append( trans.security.encode_id( repository_metadata.repository.id ) )
                         changeset_revisions.append( repository_metadata.changeset_revision )
                     new_kwd = {}
@@ -1245,6 +1247,10 @@
                                     message=message,
                                     status=status )
     @web.expose
+    def generate_workflow_image( self, trans, workflow_name, repository_metadata_id=None ):
+        """Return an svg image representation of a workflow dictionary created when the workflow was exported."""
+        return workflow_util.generate_workflow_image( trans, workflow_name, repository_metadata_id=repository_metadata_id, repository_id=None )
+    @web.expose
     def get_changeset_revision_and_ctx_rev( self, trans, **kwd ):
         """Handle a request from a local Galaxy instance to retrieve the changeset revision hash to which an installed repository can be updated."""
         params = util.Params( kwd )
@@ -1355,7 +1361,7 @@
                 repository_dependencies = suc.get_repository_dependencies_for_changeset_revision( trans=trans,
                                                                                                   repository=repository,
                                                                                                   repository_metadata=repository_metadata,
-                                                                                                  toolshed_base_url=str( url_for( '/', qualified=True ) ).rstrip( '/' ),
+                                                                                                  toolshed_base_url=str( web.url_for( '/', qualified=True ) ).rstrip( '/' ),
                                                                                                   key_rd_dicts_to_be_processed=None,
                                                                                                   all_repository_dependencies=None,
                                                                                                   handled_key_rd_dicts=None,
@@ -1418,7 +1424,7 @@
             encoded_repository_ids.append( trans.security.encode_id( repository.id ) )
             changeset_revisions.append( changeset_revision )
         if encoded_repository_ids and changeset_revisions:
-            repo_info_dict = from_json_string( self.get_repository_information( trans, encoded_repository_ids, changeset_revisions ) )
+            repo_info_dict = json.from_json_string( self.get_repository_information( trans, encoded_repository_ids, changeset_revisions ) )
         else:
             repo_info_dict = {}
         return repo_info_dict
@@ -1465,7 +1471,7 @@
                 if current_changeset_revision == changeset_revision:
                     break
         if tool_version_dicts:
-            return to_json_string( tool_version_dicts )
+            return json.to_json_string( tool_version_dicts )
         return ''
     def get_versions_of_tool( self, trans, repository, repository_metadata, guid ):
         """Return the tool lineage in descendant order for the received guid contained in the received repsitory_metadata.tool_versions."""
@@ -1595,14 +1601,14 @@
         # Redirect back to local Galaxy to perform install.
         url = suc.url_join( galaxy_url,
                             'admin_toolshed/prepare_for_install?tool_shed_url=%s&repository_ids=%s&changeset_revisions=%s' % \
-                            ( url_for( '/', qualified=True ), ','.join( util.listify( repository_ids ) ), ','.join( util.listify( changeset_revisions ) ) ) )
+                            ( web.url_for( '/', qualified=True ), ','.join( util.listify( repository_ids ) ), ','.join( util.listify( changeset_revisions ) ) ) )
         return trans.response.send_redirect( url )
     @web.expose
     def load_invalid_tool( self, trans, repository_id, tool_config, changeset_revision, **kwd ):
         params = util.Params( kwd )
         message = util.restore_text( params.get( 'message', ''  ) )
         status = params.get( 'status', 'error' )
-        repository, tool, error_message = common.load_tool_from_changeset_revision( trans, repository_id, changeset_revision, tool_config )
+        repository, tool, error_message = suc.load_tool_from_changeset_revision( trans, repository_id, changeset_revision, tool_config )
         tool_state = self.__new_state( trans )
         is_malicious = common.changeset_is_malicious( trans, repository_id, repository.tip( trans.app ) )
         invalid_file_tups = []
@@ -1701,7 +1707,7 @@
         alerts_checked = CheckboxField.is_checked( alerts )
         category_ids = util.listify( params.get( 'category_id', '' ) )
         if repository.email_alerts:
-            email_alerts = from_json_string( repository.email_alerts )
+            email_alerts = json.from_json_string( repository.email_alerts )
         else:
             email_alerts = []
         allow_push = params.get( 'allow_push', '' )
@@ -1776,12 +1782,12 @@
             if alerts_checked:
                 if user.email not in email_alerts:
                     email_alerts.append( user.email )
-                    repository.email_alerts = to_json_string( email_alerts )
+                    repository.email_alerts = json.to_json_string( email_alerts )
                     flush_needed = True
             else:
                 if user.email in email_alerts:
                     email_alerts.remove( user.email )
-                    repository.email_alerts = to_json_string( email_alerts )
+                    repository.email_alerts = json.to_json_string( email_alerts )
                     flush_needed = True
             if flush_needed:
                 trans.sa_session.add( repository )
@@ -1830,7 +1836,7 @@
                 repository_dependencies = suc.get_repository_dependencies_for_changeset_revision( trans=trans,
                                                                                                   repository=repository,
                                                                                                   repository_metadata=repository_metadata,
-                                                                                                  toolshed_base_url=str( url_for( '/', qualified=True ) ).rstrip( '/' ),
+                                                                                                  toolshed_base_url=str( web.url_for( '/', qualified=True ) ).rstrip( '/' ),
                                                                                                   key_rd_dicts_to_be_processed=None,
                                                                                                   all_repository_dependencies=None,
                                                                                                   handled_key_rd_dicts=None )
@@ -1913,7 +1919,7 @@
         Only inputs on the first page will be initialized unless `all_pages` is
         True, in which case all inputs regardless of page are initialized.
         """
-        state = DefaultToolState()
+        state = galaxy.tools.DefaultToolState()
         state.inputs = {}
         return state
     @web.json
@@ -1939,7 +1945,7 @@
             repository_dependencies = suc.get_repository_dependencies_for_changeset_revision( trans=trans,
                                                                                               repository=repository,
                                                                                               repository_metadata=repository_metadata,
-                                                                                              toolshed_base_url=str( url_for( '/', qualified=True ) ).rstrip( '/' ),
+                                                                                              toolshed_base_url=str( web.url_for( '/', qualified=True ) ).rstrip( '/' ),
                                                                                               key_rd_dicts_to_be_processed=None,
                                                                                               all_repository_dependencies=None,
                                                                                               handled_key_rd_dicts=None )
@@ -2257,18 +2263,18 @@
             for repository_id in repository_ids:
                 repository = suc.get_repository_in_tool_shed( trans, repository_id )
                 if repository.email_alerts:
-                    email_alerts = from_json_string( repository.email_alerts )
+                    email_alerts = json.from_json_string( repository.email_alerts )
                 else:
                     email_alerts = []
                 if user.email in email_alerts:
                     email_alerts.remove( user.email )
-                    repository.email_alerts = to_json_string( email_alerts )
+                    repository.email_alerts = json.to_json_string( email_alerts )
                     trans.sa_session.add( repository )
                     flush_needed = True
                     total_alerts_removed += 1
                 else:
                     email_alerts.append( user.email )
-                    repository.email_alerts = to_json_string( email_alerts )
+                    repository.email_alerts = json.to_json_string( email_alerts )
                     trans.sa_session.add( repository )
                     flush_needed = True
                     total_alerts_added += 1
@@ -2424,7 +2430,7 @@
         alerts = params.get( 'alerts', '' )
         alerts_checked = CheckboxField.is_checked( alerts )
         if repository.email_alerts:
-            email_alerts = from_json_string( repository.email_alerts )
+            email_alerts = json.from_json_string( repository.email_alerts )
         else:
             email_alerts = []
         repository_dependencies = None
@@ -2434,12 +2440,12 @@
             if alerts_checked:
                 if user.email not in email_alerts:
                     email_alerts.append( user.email )
-                    repository.email_alerts = to_json_string( email_alerts )
+                    repository.email_alerts = json.to_json_string( email_alerts )
                     flush_needed = True
             else:
                 if user.email in email_alerts:
                     email_alerts.remove( user.email )
-                    repository.email_alerts = to_json_string( email_alerts )
+                    repository.email_alerts = json.to_json_string( email_alerts )
                     flush_needed = True
             if flush_needed:
                 trans.sa_session.add( repository )
@@ -2460,7 +2466,7 @@
             repository_dependencies = suc.get_repository_dependencies_for_changeset_revision( trans=trans,
                                                                                               repository=repository,
                                                                                               repository_metadata=repository_metadata,
-                                                                                              toolshed_base_url=str( url_for( '/', qualified=True ) ).rstrip( '/' ),
+                                                                                              toolshed_base_url=str( web.url_for( '/', qualified=True ) ).rstrip( '/' ),
                                                                                               key_rd_dicts_to_be_processed=None,
                                                                                               all_repository_dependencies=None,
                                                                                               handled_key_rd_dicts=None )
@@ -2527,7 +2533,7 @@
                             guid = tool_metadata_dict[ 'guid' ]
                             full_path_to_tool_config = os.path.abspath( relative_path_to_tool_config )
                             full_path_to_dir, tool_config_filename = os.path.split( full_path_to_tool_config )
-                            can_use_disk_file = common.can_use_tool_config_disk_file( trans, repository, repo, full_path_to_tool_config, changeset_revision )
+                            can_use_disk_file = suc.can_use_tool_config_disk_file( trans, repository, repo, full_path_to_tool_config, changeset_revision )
                             if can_use_disk_file:
                                 trans.app.config.tool_data_path = work_dir
                                 tool, valid, message, sample_files = suc.handle_sample_files_and_load_tool_from_disk( trans,
@@ -2576,7 +2582,26 @@
                                     review_id=review_id,
                                     message=message,
                                     status=status )
-
+    @web.expose
+    def view_workflow( self, trans, workflow_name, repository_metadata_id, **kwd ):
+        """Retrieve necessary information about a workflow from the database so that it can be displayed in an svg image."""
+        params = util.Params( kwd )
+        message = util.restore_text( params.get( 'message', ''  ) )
+        status = params.get( 'status', 'done' )
+        if workflow_name:
+            workflow_name = encoding_util.tool_shed_decode( workflow_name )
+        repository_metadata = suc.get_repository_metadata_by_id( trans, repository_metadata_id )
+        repository = suc.get_repository_in_tool_shed( trans, trans.security.encode_id( repository_metadata.repository_id ) )
+        changeset_revision = repository_metadata.changeset_revision
+        metadata = repository_metadata.metadata
+        return trans.fill_template( "/webapps/community/repository/view_workflow.mako",
+                                    repository=repository,
+                                    changeset_revision=changeset_revision,
+                                    repository_metadata_id=repository_metadata_id,
+                                    workflow_name=workflow_name,
+                                    metadata=metadata,
+                                    message=message,
+                                    status=status )
 # ----- Utility methods -----
 
 def build_changeset_revision_select_field( trans, repository, selected_value=None, add_id_to_name=True,


diff -r 875ac898df00fd919b6b24f58562fadbf03dc5e1 -r 7073d786cad0f0d251d4ea9b2c42171f698cf953 lib/galaxy/webapps/community/controllers/workflow.py
--- a/lib/galaxy/webapps/community/controllers/workflow.py
+++ /dev/null
@@ -1,411 +0,0 @@
-import pkg_resources
-pkg_resources.require( "simplejson" )
-pkg_resources.require( "SVGFig" )
-import os, logging, ConfigParser, tempfile, shutil, svgfig
-from galaxy.webapps.community import model
-from galaxy.web.framework.helpers import time_ago, iff, grids
-from galaxy.util.json import from_json_string, to_json_string
-from galaxy.workflow.modules import InputDataModule, ToolModule, WorkflowModuleFactory
-from galaxy.web.base.controller import *
-from galaxy.tools import DefaultToolState
-from galaxy.webapps.galaxy.controllers.workflow import attach_ordered_steps
-import common
-import galaxy.util.shed_util_common as suc
-from galaxy.tool_shed import encoding_util
-
-class RepoInputDataModule( InputDataModule ):
-
-    type = "data_input"
-    name = "Input dataset"
-
-    @classmethod
-    def new( Class, trans, tools_metadata=None, tool_id=None ):
-        module = Class( trans )
-        module.state = dict( name="Input Dataset" )
-        return module
-    @classmethod
-    def from_dict( Class, trans, repository_id, changeset_revision, step_dict, tools_metadata=None, secure=True ):
-        module = Class( trans )
-        state = from_json_string( step_dict[ "tool_state" ] )
-        module.state = dict( name=state.get( "name", "Input Dataset" ) )
-        return module
-    @classmethod
-    def from_workflow_step( Class, trans, repository_id, changeset_revision, tools_metadata, step ):
-        module = Class( trans )
-        module.state = dict( name="Input Dataset" )
-        if step.tool_inputs and "name" in step.tool_inputs:
-            module.state[ 'name' ] = step.tool_inputs[ 'name' ]
-        return module
-
-class RepoToolModule( ToolModule ):
-    
-    type = "tool"
-    
-    def __init__( self, trans, repository_id, changeset_revision, tools_metadata, tool_id ):
-        self.trans = trans
-        self.tools_metadata = tools_metadata
-        self.tool_id = tool_id
-        self.tool = None
-        self.errors = None
-        for tool_dict in tools_metadata:
-            if self.tool_id in [ tool_dict[ 'id' ], tool_dict[ 'guid' ] ]:
-                repository, self.tool, message = common.load_tool_from_changeset_revision( trans, repository_id, changeset_revision, tool_dict[ 'tool_config' ] )
-                if message and self.tool is None:
-                    self.errors = 'unavailable'
-                break
-        self.post_job_actions = {}
-        self.workflow_outputs = []
-        self.state = None
-    @classmethod
-    def new( Class, trans, repository_id, changeset_revision, tools_metadata, tool_id=None ):
-        module = Class( trans, repository_id, changeset_revision, tools_metadata, tool_id )
-        module.state = module.tool.new_state( trans, all_pages=True )
-        return module
-    @classmethod
-    def from_dict( Class, trans, repository_id, changeset_revision, step_dict, tools_metadata, secure=True ):
-        tool_id = step_dict[ 'tool_id' ]
-        module = Class( trans, repository_id, changeset_revision, tools_metadata, tool_id )
-        module.state = DefaultToolState()
-        if module.tool is not None:
-            module.state.decode( step_dict[ "tool_state" ], module.tool, module.trans.app, secure=secure )
-        module.errors = step_dict.get( "tool_errors", None )
-        return module
-    @classmethod
-    def from_workflow_step( Class, trans, repository_id, changeset_revision, tools_metadata, step ):
-        module = Class( trans, repository_id, changeset_revision, tools_metadata, step.tool_id )
-        module.state = DefaultToolState()
-        if module.tool:
-            module.state.inputs = module.tool.params_from_strings( step.tool_inputs, trans.app, ignore_errors=True )
-        else:
-            module.state.inputs = {}
-        module.errors = step.tool_errors
-        return module
-    def get_data_inputs( self ):
-        data_inputs = []
-        def callback( input, value, prefixed_name, prefixed_label ):
-            if isinstance( input, DataToolParameter ):
-                data_inputs.append( dict( name=prefixed_name,
-                                          label=prefixed_label,
-                                          extensions=input.extensions ) )
-        if self.tool:
-            visit_input_values( self.tool.inputs, self.state.inputs, callback )
-        return data_inputs
-    def get_data_outputs( self ):
-        data_outputs = []
-        if self.tool:
-            data_inputs = None
-            for name, tool_output in self.tool.outputs.iteritems():
-                if tool_output.format_source != None:
-                    # Default to special name "input" which remove restrictions on connections
-                    formats = [ 'input' ]
-                    if data_inputs == None:
-                        data_inputs = self.get_data_inputs()
-                    # Find the input parameter referenced by format_source
-                    for di in data_inputs:
-                        # Input names come prefixed with conditional and repeat names separated by '|',
-                        # so remove prefixes when comparing with format_source.
-                        if di[ 'name' ] != None and di[ 'name' ].split( '|' )[ -1 ] == tool_output.format_source:
-                            formats = di[ 'extensions' ]
-                else:
-                    formats = [ tool_output.format ]
-                for change_elem in tool_output.change_format:
-                    for when_elem in change_elem.findall( 'when' ):
-                        format = when_elem.get( 'format', None )
-                        if format and format not in formats:
-                            formats.append( format )
-                data_outputs.append( dict( name=name, extensions=formats ) )
-        return data_outputs
-
-class RepoWorkflowModuleFactory( WorkflowModuleFactory ):
-    def __init__( self, module_types ):
-        self.module_types = module_types
-    def new( self, trans, type, tools_metadata=None, tool_id=None ):
-        """Return module for type and (optional) tool_id initialized with new / default state."""
-        assert type in self.module_types
-        return self.module_types[type].new( trans, tool_id )
-    def from_dict( self, trans, repository_id, changeset_revision, step_dict, **kwd ):
-        """Return module initialized from the data in dictionary `step_dict`."""
-        type = step_dict[ 'type' ]
-        assert type in self.module_types
-        return self.module_types[ type ].from_dict( trans, repository_id, changeset_revision, step_dict, **kwd )
-    def from_workflow_step( self, trans, repository_id, changeset_revision, tools_metadata, step ):
-        """Return module initialized from the WorkflowStep object `step`."""
-        type = step.type
-        return self.module_types[ type ].from_workflow_step( trans, repository_id, changeset_revision, tools_metadata, step )
-
-module_factory = RepoWorkflowModuleFactory( dict( data_input=RepoInputDataModule, tool=RepoToolModule ) )
-
-class WorkflowController( BaseUIController ):
-    @web.expose
-    def view_workflow( self, trans, **kwd ):
-        repository_metadata_id = kwd.get( 'repository_metadata_id', '' )
-        workflow_name = kwd.get( 'workflow_name', '' )
-        if workflow_name:
-            workflow_name = encoding_util.tool_shed_decode( workflow_name )
-        message = kwd.get( 'message', '' )
-        status = kwd.get( 'status', 'done' )
-        repository_metadata = common.get_repository_metadata_by_id( trans, repository_metadata_id )
-        repository = suc.get_repository_in_tool_shed( trans, trans.security.encode_id( repository_metadata.repository_id ) )
-        return trans.fill_template( "/webapps/community/repository/view_workflow.mako",
-                                    repository=repository,
-                                    changeset_revision=repository_metadata.changeset_revision,
-                                    repository_metadata_id=repository_metadata_id,
-                                    workflow_name=workflow_name,
-                                    metadata=repository_metadata.metadata,
-                                    message=message,
-                                    status=status )
-    @web.expose
-    def generate_workflow_image( self, trans, repository_metadata_id, workflow_name ):
-        repository_metadata = common.get_repository_metadata_by_id( trans, repository_metadata_id )
-        repository_id = trans.security.encode_id( repository_metadata.repository_id )
-        changeset_revision = repository_metadata.changeset_revision
-        metadata = repository_metadata.metadata
-        workflow_name = encoding_util.tool_shed_decode( workflow_name )
-        # metadata[ 'workflows' ] is a list of tuples where each contained tuple is
-        # [ <relative path to the .ga file in the repository>, <exported workflow dict> ]
-        for workflow_tup in metadata[ 'workflows' ]:
-            workflow_dict = workflow_tup[1]
-            if workflow_dict[ 'name' ] == workflow_name:
-                break
-        if 'tools' in metadata:
-            tools_metadata = metadata[ 'tools' ]
-        else:
-            tools_metadata = []
-        workflow, missing_tool_tups = self.__workflow_from_dict( trans, workflow_dict, tools_metadata, repository_id, changeset_revision )
-        data = []
-        canvas = svgfig.canvas( style="stroke:black; fill:none; stroke-width:1px; stroke-linejoin:round; text-anchor:left" )
-        text = svgfig.SVG( "g" )
-        connectors = svgfig.SVG( "g" )
-        boxes = svgfig.SVG( "g" )
-        svgfig.Text.defaults[ "font-size" ] = "10px"
-        in_pos = {}
-        out_pos = {}
-        margin = 5
-        # Spacing between input/outputs.
-        line_px = 16
-        # Store px width for boxes of each step.
-        widths = {}
-        max_width, max_x, max_y = 0, 0, 0
-        for step in workflow.steps:
-            step.upgrade_messages = {}
-            module = module_factory.from_workflow_step( trans, repository_id, changeset_revision, tools_metadata, step )
-            tool_errors = module.type == 'tool' and not module.tool
-            module_data_inputs = self.__get_data_inputs( step, module )
-            module_data_outputs = self.__get_data_outputs( step, module, workflow.steps )
-            step_dict = {
-                'id' : step.order_index,
-                'data_inputs' : module_data_inputs,
-                'data_outputs' : module_data_outputs,
-                'position' : step.position,
-                'tool_errors' : tool_errors
-            }
-            input_conn_dict = {}
-            for conn in step.input_connections:
-                input_conn_dict[ conn.input_name ] = dict( id=conn.output_step.order_index, output_name=conn.output_name )
-            step_dict[ 'input_connections' ] = input_conn_dict
-            data.append( step_dict )
-            x, y = step.position[ 'left' ], step.position[ 'top' ]
-            count = 0
-            module_name = self.__get_name( module, missing_tool_tups )
-            max_len = len( module_name ) * 1.5
-            text.append( svgfig.Text( x, y + 20, module_name, **{ "font-size": "14px" } ).SVG() )
-            y += 45
-            for di in module_data_inputs:
-                cur_y = y + count * line_px
-                if step.order_index not in in_pos:
-                    in_pos[ step.order_index ] = {}
-                in_pos[ step.order_index ][ di[ 'name' ] ] = ( x, cur_y )
-                text.append( svgfig.Text( x, cur_y, di[ 'label' ] ).SVG() )
-                count += 1
-                max_len = max( max_len, len( di[ 'label' ] ) )
-            if len( module.get_data_inputs() ) > 0:
-                y += 15
-            for do in module_data_outputs:
-                cur_y = y + count * line_px
-                if step.order_index not in out_pos:
-                    out_pos[ step.order_index ] = {}
-                out_pos[ step.order_index ][ do[ 'name' ] ] = ( x, cur_y )
-                text.append( svgfig.Text( x, cur_y, do[ 'name' ] ).SVG() )
-                count += 1
-                max_len = max( max_len, len( do['name' ] ) )
-            widths[ step.order_index ] = max_len * 5.5
-            max_x = max( max_x, step.position[ 'left' ] )
-            max_y = max( max_y, step.position[ 'top' ] )
-            max_width = max( max_width, widths[ step.order_index ] )
-        for step_dict in data:
-            tool_unavailable = step_dict[ 'tool_errors' ]
-            width = widths[ step_dict[ 'id' ] ]
-            x, y = step_dict[ 'position' ][ 'left' ], step_dict[ 'position' ][ 'top' ]
-            if tool_unavailable:
-                fill = "#EBBCB2"
-            else:
-                fill = "#EBD9B2"    
-            boxes.append( svgfig.Rect( x - margin, y, x + width - margin, y + 30, fill=fill ).SVG() )
-            box_height = ( len( step_dict[ 'data_inputs' ] ) + len( step_dict[ 'data_outputs' ] ) ) * line_px + margin
-            # Draw separator line.
-            if len( step_dict[ 'data_inputs' ] ) > 0:
-                box_height += 15
-                sep_y = y + len( step_dict[ 'data_inputs' ] ) * line_px + 40
-                text.append( svgfig.Line( x - margin, sep_y, x + width - margin, sep_y ).SVG() )
-            # Define an input/output box.
-            boxes.append( svgfig.Rect( x - margin, y + 30, x + width - margin, y + 30 + box_height, fill="#ffffff" ).SVG() )
-            for conn, output_dict in step_dict[ 'input_connections' ].iteritems():
-                in_coords = in_pos[ step_dict[ 'id' ] ][ conn ]
-                # out_pos_index will be a step number like 1, 2, 3...
-                out_pos_index = output_dict[ 'id' ]
-                # out_pos_name will be a string like 'o', 'o2', etc.
-                out_pos_name = output_dict[ 'output_name' ]
-                if out_pos_index in out_pos:
-                    # out_conn_index_dict will be something like:
-                    # 7: {'o': (824.5, 618)}
-                    out_conn_index_dict = out_pos[ out_pos_index ]
-                    if out_pos_name in out_conn_index_dict:
-                        out_conn_pos = out_pos[ out_pos_index ][ out_pos_name ]
-                    else:
-                        # Take any key / value pair available in out_conn_index_dict.
-                        # A problem will result if the dictionary is empty.
-                        if out_conn_index_dict.keys():
-                            key = out_conn_index_dict.keys()[0]
-                            out_conn_pos = out_pos[ out_pos_index ][ key ]
-                adjusted = ( out_conn_pos[ 0 ] + widths[ output_dict[ 'id' ] ], out_conn_pos[ 1 ] )
-                text.append( svgfig.SVG( "circle",
-                                         cx=out_conn_pos[ 0 ] + widths[ output_dict[ 'id' ] ] - margin,
-                                         cy=out_conn_pos[ 1 ] - margin,
-                                         r = 5,
-                                         fill="#ffffff" ) )
-                connectors.append( svgfig.Line( adjusted[ 0 ],
-                                                adjusted[ 1 ] - margin,
-                                                in_coords[ 0 ] - 10,
-                                                in_coords[ 1 ],
-                                                arrow_end = "true" ).SVG() )
-        canvas.append( connectors )
-        canvas.append( boxes )
-        canvas.append( text )
-        width, height = ( max_x + max_width + 50 ), max_y + 300
-        canvas[ 'width' ] = "%s px" % width
-        canvas[ 'height' ] = "%s px" % height
-        canvas[ 'viewBox' ] = "0 0 %s %s" % ( width, height )
-        trans.response.set_content_type( "image/svg+xml" )
-        return canvas.standalone_xml()
-    def __get_name( self, module, missing_tool_tups ):
-        module_name = module.get_name()
-        if module.type == 'tool' and module_name == 'unavailable':
-            for missing_tool_tup in missing_tool_tups:
-                missing_tool_id, missing_tool_name, missing_tool_version = missing_tool_tup
-                if missing_tool_id == module.tool_id:
-                    module_name = '%s' % missing_tool_name
-        return module_name
-    def __get_data_inputs( self, step, module ):
-        if module.type == 'tool':
-            if module.tool:
-                return module.get_data_inputs()
-            else:
-                data_inputs = []
-                for wfsc in step.input_connections:
-                    data_inputs_dict = {}
-                    data_inputs_dict[ 'extensions' ] = [ '' ]
-                    data_inputs_dict[ 'name' ] = wfsc.input_name
-                    data_inputs_dict[ 'label' ] = 'Unknown'
-                    data_inputs.append( data_inputs_dict )
-                return data_inputs
-        return module.get_data_inputs()
-    def __get_data_outputs( self, step, module, steps ):
-        if module.type == 'tool':
-            if module.tool:
-                return module.get_data_outputs()
-            else:
-                data_outputs = []
-                data_outputs_dict = {}
-                data_outputs_dict[ 'extensions' ] = [ 'input' ]
-                found = False
-                for workflow_step in steps:
-                    for wfsc in workflow_step.input_connections:
-                        if step.name == wfsc.output_step.name:
-                            data_outputs_dict[ 'name' ] = wfsc.output_name
-                            found = True
-                            break
-                    if found:
-                        break
-                if not found:
-                    # We're at the last step of the workflow.
-                    data_outputs_dict[ 'name' ] = 'output'
-                data_outputs.append( data_outputs_dict )       
-                return data_outputs
-        return module.get_data_outputs()
-    def __workflow_from_dict( self, trans, workflow_dict, tools_metadata, repository_id, changeset_revision ):
-        """Creates and returns workflow object from a dictionary."""
-        trans.workflow_building_mode = True
-        workflow = model.Workflow()
-        workflow.name = workflow_dict[ 'name' ]
-        workflow.has_errors = False
-        steps = []
-        # Keep ids for each step that we need to use to make connections.
-        steps_by_external_id = {}
-        # Keep track of tools required by the workflow that are not available in
-        # the tool shed repository.  Each tuple in the list of missing_tool_tups
-        # will be ( tool_id, tool_name, tool_version ).
-        missing_tool_tups = []
-        # First pass to build step objects and populate basic values
-        for key, step_dict in workflow_dict[ 'steps' ].iteritems():
-            # Create the model class for the step
-            step = model.WorkflowStep()
-            step.name = step_dict[ 'name' ]
-            step.position = step_dict[ 'position' ]
-            module = module_factory.from_dict( trans, repository_id, changeset_revision, step_dict, tools_metadata=tools_metadata, secure=False )
-            if module.type == 'tool' and module.tool is None:
-                # A required tool is not available in the current repository.
-                step.tool_errors = 'unavailable'
-                missing_tool_tup = ( step_dict[ 'tool_id' ], step_dict[ 'name' ], step_dict[ 'tool_version' ] )
-                if missing_tool_tup not in missing_tool_tups:
-                    missing_tool_tups.append( missing_tool_tup )
-            module.save_to_step( step )
-            if step.tool_errors:
-                workflow.has_errors = True
-            # Stick this in the step temporarily.
-            step.temp_input_connections = step_dict[ 'input_connections' ]
-            steps.append( step )
-            steps_by_external_id[ step_dict[ 'id' ] ] = step
-        # Second pass to deal with connections between steps.
-        for step in steps:
-            # Input connections.
-            for input_name, conn_dict in step.temp_input_connections.iteritems():
-                if conn_dict:
-                    output_step = steps_by_external_id[ conn_dict[ 'id' ] ]
-                    conn = model.WorkflowStepConnection()
-                    conn.input_step = step
-                    conn.input_name = input_name
-                    conn.output_step = output_step
-                    conn.output_name = conn_dict[ 'output_name' ]
-                    step.input_connections.append( conn )
-            del step.temp_input_connections
-        # Order the steps if possible.
-        attach_ordered_steps( workflow, steps )
-        return workflow, missing_tool_tups
-    @web.expose
-    def import_workflow( self, trans, **kwd ):
-        repository_metadata_id = kwd.get( 'repository_metadata_id', '' )
-        workflow_name = kwd.get( 'workflow_name', '' )
-        if workflow_name:
-            workflow_name = encoding_util.tool_shed_decode( workflow_name )
-        message = kwd.get( 'message', '' )
-        status = kwd.get( 'status', 'done' )
-        repository_metadata = get_repository_metadata_by_id( trans, repository_metadata_id )
-        workflows = repository_metadata.metadata[ 'workflows' ]
-        workflow_data = None
-        for workflow_data in workflows:
-            if workflow_data[ 'name' ] == workflow_name:
-                break
-        if workflow_data:
-            if kwd.get( 'open_for_url', False ):
-                tmp_fd, tmp_fname = tempfile.mkstemp()
-                to_file = open( tmp_fname, 'wb' )
-                to_file.write( to_json_string( workflow_data ) )
-                return open( tmp_fname )
-            galaxy_url = trans.get_cookie( name='toolshedgalaxyurl' )
-            url = '%sworkflow/import_workflow?tool_shed_url=%s&repository_metadata_id=%s&workflow_name=%s' % \
-                ( galaxy_url, url_for( '/', qualified=True ), repository_metadata_id, encoding_util.tool_shed_encode( workflow_name ) )
-            return trans.response.send_redirect( url )
-        return trans.response.send_redirect( web.url_for( controller='workflow',
-                                                          action='view_workflow',
-                                                          message=message,
-                                                          status=status ) )


diff -r 875ac898df00fd919b6b24f58562fadbf03dc5e1 -r 7073d786cad0f0d251d4ea9b2c42171f698cf953 lib/galaxy/webapps/community/util/container_util.py
--- a/lib/galaxy/webapps/community/util/container_util.py
+++ b/lib/galaxy/webapps/community/util/container_util.py
@@ -56,11 +56,12 @@
 
 class InvalidTool( object ):
     """Invalid tool object"""
-    def __init__( self, id=None, tool_config=None, repository_id=None, changeset_revision=None ):
+    def __init__( self, id=None, tool_config=None, repository_id=None, changeset_revision=None, repository_installation_status=None ):
         self.id = id
         self.tool_config = tool_config
         self.repository_id = repository_id
         self.changeset_revision = changeset_revision
+        self.repository_installation_status = repository_installation_status
 
 class ReadMe( object ):
     """Readme text object"""
@@ -86,7 +87,7 @@
 class Tool( object ):
     """Tool object"""
     def __init__( self, id=None, tool_config=None, tool_id=None, name=None, description=None, version=None, requirements=None,
-                  repository_id=None, changeset_revision=None ):
+                  repository_id=None, changeset_revision=None, repository_installation_status=None ):
         self.id = id
         self.tool_config = tool_config
         self.tool_id = tool_id
@@ -96,6 +97,7 @@
         self.requirements = requirements
         self.repository_id = repository_id
         self.changeset_revision = changeset_revision
+        self.repository_installation_status = repository_installation_status
 
 class ToolDependency( object ):
     """Tool dependency object"""
@@ -112,14 +114,17 @@
         self.tool_dependency_id = tool_dependency_id
 
 class Workflow( object ):
-    """Workflow object"""
-    def __init__( self, id=None, repository_metadata_id=None, workflow_name=None, steps=None, format_version=None, annotation=None ):
+    """Workflow object."""
+    def __init__( self, id=None, workflow_name=None, steps=None, format_version=None, annotation=None, repository_metadata_id=None, repository_id=None ):
+        # When rendered in the tool shed, repository_metadata_id will have a value and repository_id will be None.  When rendered in Galaxy, repository_id
+        # will have a value and repository_metadata_id will be None.
         self.id = id
-        self.repository_metadata_id = repository_metadata_id
         self.workflow_name = workflow_name
         self.steps = steps
         self.format_version = format_version
         self.annotation = annotation
+        self.repository_metadata_id = repository_metadata_id
+        self.repository_id = repository_id
 
 def build_datatypes_folder( trans, folder_id, datatypes, label='Datatypes' ):
     """Return a folder hierarchy containing datatypes."""
@@ -163,12 +168,18 @@
             invalid_tool_id += 1
             if repository:
                 repository_id = repository.id
+                if trans.webapp.name == 'galaxy':
+                    repository_installation_status = repository.status
+                else:
+                    repository_installation_status = None
             else:
                 repository_id = None
+                repository_installation_status = None
             invalid_tool = InvalidTool( id=invalid_tool_id,
                                         tool_config=invalid_tool_config,
                                         repository_id=repository_id,
-                                        changeset_revision=changeset_revision )
+                                        changeset_revision=changeset_revision,
+                                        repository_installation_status=repository_installation_status )
             folder.invalid_tools.append( invalid_tool )
     else:
         invalid_tools_root_folder = None
@@ -249,8 +260,13 @@
         folder.valid_tools.append( tool )
         if repository:
             repository_id = repository.id
+            if trans.webapp.name == 'galaxy':
+                repository_installation_status = repository.status
+            else:
+                repository_installation_status = None
         else:
-            repository_id = ''
+            repository_id = None
+            repository_installation_status = None
         for tool_dict in tool_dicts:
             tool_id += 1
             if 'requirements' in tool_dict:
@@ -269,7 +285,8 @@
                          version=tool_dict[ 'version' ],
                          requirements=requirements_str,
                          repository_id=repository_id,
-                         changeset_revision=changeset_revision )
+                         changeset_revision=changeset_revision,
+                         repository_installation_status=repository_installation_status )
             folder.valid_tools.append( tool )
     else:
         tools_root_folder = None
@@ -351,8 +368,13 @@
     else:
         tool_dependencies_root_folder = None
     return folder_id, tool_dependencies_root_folder
-def build_workflows_folder( trans, folder_id, workflows, repository_metadata, label='Workflows' ):
-    """Return a folder hierarchy containing invalid tools."""
+def build_workflows_folder( trans, folder_id, workflows, repository_metadata_id=None, repository_id=None, label='Workflows' ):
+    """
+    Return a folder hierarchy containing workflow objects for each workflow dictionary in the received workflows list.  When
+    this method is called from the tool shed, repository_metadata_id will have a value and repository_id will be None.  When
+    this method is called from Galaxy, repository_id will have a value only if the repository is not currenlty being installed
+    and repository_metadata_id will be None.
+    """
     if workflows:
         workflow_id = 0
         folder_id += 1
@@ -363,11 +385,12 @@
         # Insert a header row.
         workflow_id += 1
         workflow = Workflow( id=workflow_id,
-                             repository_metadata_id=None,
                              workflow_name='Name',
                              steps='steps',
                              format_version='format-version',
-                             annotation='annotation' )
+                             annotation='annotation',
+                             repository_metadata_id=repository_metadata_id,
+                             repository_id=repository_id )
         folder.workflows.append( workflow )
         for workflow_tup in workflows:
             workflow_dict=workflow_tup[ 1 ]
@@ -378,11 +401,12 @@
                 steps = 'unknown'
             workflow_id += 1
             workflow = Workflow( id=workflow_id,
-                                 repository_metadata_id=repository_metadata.id,
                                  workflow_name=workflow_dict[ 'name' ],
                                  steps=steps,
                                  format_version=workflow_dict[ 'format-version' ],
-                                 annotation=workflow_dict[ 'annotation' ] )
+                                 annotation=workflow_dict[ 'annotation' ],
+                                 repository_metadata_id=repository_metadata_id,
+                                 repository_id=repository_id )
             folder.workflows.append( workflow )
     else:
         workflows_root_folder = None


diff -r 875ac898df00fd919b6b24f58562fadbf03dc5e1 -r 7073d786cad0f0d251d4ea9b2c42171f698cf953 lib/galaxy/webapps/community/util/workflow_util.py
--- /dev/null
+++ b/lib/galaxy/webapps/community/util/workflow_util.py
@@ -0,0 +1,384 @@
+from galaxy import eggs
+import pkg_resources
+
+pkg_resources.require( "SVGFig" )
+
+import logging, svgfig
+from galaxy.util import json
+import galaxy.util.shed_util_common as suc
+from galaxy.tool_shed import encoding_util
+from galaxy.workflow.modules import InputDataModule, ToolModule, WorkflowModuleFactory
+import galaxy.webapps.galaxy.controllers.workflow
+import galaxy.tools
+import galaxy.tools.parameters
+
+log = logging.getLogger( __name__ )
+
+class RepoInputDataModule( InputDataModule ):
+
+    type = "data_input"
+    name = "Input dataset"
+
+    @classmethod
+    def new( Class, trans, tools_metadata=None, tool_id=None ):
+        module = Class( trans )
+        module.state = dict( name="Input Dataset" )
+        return module
+    @classmethod
+    def from_dict( Class, trans, repository_id, changeset_revision, step_dict, tools_metadata=None, secure=True ):
+        module = Class( trans )
+        state = json.from_json_string( step_dict[ "tool_state" ] )
+        module.state = dict( name=state.get( "name", "Input Dataset" ) )
+        return module
+    @classmethod
+    def from_workflow_step( Class, trans, repository_id, changeset_revision, tools_metadata, step ):
+        module = Class( trans )
+        module.state = dict( name="Input Dataset" )
+        if step.tool_inputs and "name" in step.tool_inputs:
+            module.state[ 'name' ] = step.tool_inputs[ 'name' ]
+        return module
+
+class RepoToolModule( ToolModule ):
+    
+    type = "tool"
+    
+    def __init__( self, trans, repository_id, changeset_revision, tools_metadata, tool_id ):
+        self.trans = trans
+        self.tools_metadata = tools_metadata
+        self.tool_id = tool_id
+        self.tool = None
+        self.errors = None
+        for tool_dict in tools_metadata:
+            if self.tool_id in [ tool_dict[ 'id' ], tool_dict[ 'guid' ] ]:
+                if trans.webapp.name == 'community':
+                    # We're in the tool shed.
+                    repository, self.tool, message = suc.load_tool_from_changeset_revision( trans, repository_id, changeset_revision, tool_dict[ 'tool_config' ] )
+                    if message and self.tool is None:
+                        self.errors = 'unavailable'
+                    break
+                else:
+                    # We're in Galaxy.
+                    self.tool = trans.app.toolbox.tools_by_id.get( self.tool_id, None )
+                    if self.tool is None:
+                        self.errors = 'unavailable'
+        self.post_job_actions = {}
+        self.workflow_outputs = []
+        self.state = None
+    @classmethod
+    def new( Class, trans, repository_id, changeset_revision, tools_metadata, tool_id=None ):
+        module = Class( trans, repository_id, changeset_revision, tools_metadata, tool_id )
+        module.state = module.tool.new_state( trans, all_pages=True )
+        return module
+    @classmethod
+    def from_dict( Class, trans, repository_id, changeset_revision, step_dict, tools_metadata, secure=True ):
+        tool_id = step_dict[ 'tool_id' ]
+        module = Class( trans, repository_id, changeset_revision, tools_metadata, tool_id )
+        module.state = galaxy.tools.DefaultToolState()
+        if module.tool is not None:
+            module.state.decode( step_dict[ "tool_state" ], module.tool, module.trans.app, secure=secure )
+        module.errors = step_dict.get( "tool_errors", None )
+        return module
+    @classmethod
+    def from_workflow_step( Class, trans, repository_id, changeset_revision, tools_metadata, step ):
+        module = Class( trans, repository_id, changeset_revision, tools_metadata, step.tool_id )
+        module.state = galaxy.tools.DefaultToolState()
+        if module.tool:
+            module.state.inputs = module.tool.params_from_strings( step.tool_inputs, trans.app, ignore_errors=True )
+        else:
+            module.state.inputs = {}
+        module.errors = step.tool_errors
+        return module
+    def get_data_inputs( self ):
+        data_inputs = []
+        def callback( input, value, prefixed_name, prefixed_label ):
+            if isinstance( input, galaxy.tools.parameters.DataToolParameter ):
+                data_inputs.append( dict( name=prefixed_name,
+                                          label=prefixed_label,
+                                          extensions=input.extensions ) )
+        if self.tool:
+            galaxy.tools.parameters.visit_input_values( self.tool.inputs, self.state.inputs, callback )
+        return data_inputs
+    def get_data_outputs( self ):
+        data_outputs = []
+        if self.tool:
+            data_inputs = None
+            for name, tool_output in self.tool.outputs.iteritems():
+                if tool_output.format_source != None:
+                    # Default to special name "input" which remove restrictions on connections
+                    formats = [ 'input' ]
+                    if data_inputs == None:
+                        data_inputs = self.get_data_inputs()
+                    # Find the input parameter referenced by format_source
+                    for di in data_inputs:
+                        # Input names come prefixed with conditional and repeat names separated by '|',
+                        # so remove prefixes when comparing with format_source.
+                        if di[ 'name' ] != None and di[ 'name' ].split( '|' )[ -1 ] == tool_output.format_source:
+                            formats = di[ 'extensions' ]
+                else:
+                    formats = [ tool_output.format ]
+                for change_elem in tool_output.change_format:
+                    for when_elem in change_elem.findall( 'when' ):
+                        format = when_elem.get( 'format', None )
+                        if format and format not in formats:
+                            formats.append( format )
+                data_outputs.append( dict( name=name, extensions=formats ) )
+        return data_outputs
+
+class RepoWorkflowModuleFactory( WorkflowModuleFactory ):
+    def __init__( self, module_types ):
+        self.module_types = module_types
+    def new( self, trans, type, tools_metadata=None, tool_id=None ):
+        """Return module for type and (optional) tool_id initialized with new / default state."""
+        assert type in self.module_types
+        return self.module_types[type].new( trans, tool_id )
+    def from_dict( self, trans, repository_id, changeset_revision, step_dict, **kwd ):
+        """Return module initialized from the data in dictionary `step_dict`."""
+        type = step_dict[ 'type' ]
+        assert type in self.module_types
+        return self.module_types[ type ].from_dict( trans, repository_id, changeset_revision, step_dict, **kwd )
+    def from_workflow_step( self, trans, repository_id, changeset_revision, tools_metadata, step ):
+        """Return module initialized from the WorkflowStep object `step`."""
+        type = step.type
+        return self.module_types[ type ].from_workflow_step( trans, repository_id, changeset_revision, tools_metadata, step )
+
+module_factory = RepoWorkflowModuleFactory( dict( data_input=RepoInputDataModule, tool=RepoToolModule ) )
+
+def generate_workflow_image( trans, workflow_name, repository_metadata_id=None, repository_id=None ):
+    """
+    Return an svg image representation of a workflow dictionary created when the workflow was exported.  This method is called
+    from both Galaxy and the tool shed.  When called from the tool shed, repository_metadata_id will have a value and repository_id
+    will be None.  When called from Galaxy, repository_metadata_id will be None and repository_id will have a value.
+    """
+    workflow_name = encoding_util.tool_shed_decode( workflow_name )
+    if trans.webapp.name == 'community':
+        # We're in the tool shed.
+        repository_metadata = suc.get_repository_metadata_by_id( trans, repository_metadata_id )
+        repository_id = trans.security.encode_id( repository_metadata.repository_id )
+        changeset_revision = repository_metadata.changeset_revision
+        metadata = repository_metadata.metadata
+    else:
+        # We're in Galaxy.
+        repository = suc.get_tool_shed_repository_by_id( trans, repository_id )
+        changeset_revision = repository.changeset_revision
+        metadata = repository.metadata
+    # metadata[ 'workflows' ] is a list of tuples where each contained tuple is
+    # [ <relative path to the .ga file in the repository>, <exported workflow dict> ]
+    for workflow_tup in metadata[ 'workflows' ]:
+        workflow_dict = workflow_tup[1]
+        if workflow_dict[ 'name' ] == workflow_name:
+            break
+    if 'tools' in metadata:
+        tools_metadata = metadata[ 'tools' ]
+    else:
+        tools_metadata = []
+    workflow, missing_tool_tups = get_workflow_from_dict( trans, workflow_dict, tools_metadata, repository_id, changeset_revision )
+    data = []
+    canvas = svgfig.canvas( style="stroke:black; fill:none; stroke-width:1px; stroke-linejoin:round; text-anchor:left" )
+    text = svgfig.SVG( "g" )
+    connectors = svgfig.SVG( "g" )
+    boxes = svgfig.SVG( "g" )
+    svgfig.Text.defaults[ "font-size" ] = "10px"
+    in_pos = {}
+    out_pos = {}
+    margin = 5
+    # Spacing between input/outputs.
+    line_px = 16
+    # Store px width for boxes of each step.
+    widths = {}
+    max_width, max_x, max_y = 0, 0, 0
+    for step in workflow.steps:
+        step.upgrade_messages = {}
+        module = module_factory.from_workflow_step( trans, repository_id, changeset_revision, tools_metadata, step )
+        tool_errors = module.type == 'tool' and not module.tool
+        module_data_inputs = get_workflow_data_inputs( step, module )
+        module_data_outputs = get_workflow_data_outputs( step, module, workflow.steps )
+        step_dict = {
+            'id' : step.order_index,
+            'data_inputs' : module_data_inputs,
+            'data_outputs' : module_data_outputs,
+            'position' : step.position,
+            'tool_errors' : tool_errors
+        }
+        input_conn_dict = {}
+        for conn in step.input_connections:
+            input_conn_dict[ conn.input_name ] = dict( id=conn.output_step.order_index, output_name=conn.output_name )
+        step_dict[ 'input_connections' ] = input_conn_dict
+        data.append( step_dict )
+        x, y = step.position[ 'left' ], step.position[ 'top' ]
+        count = 0
+        module_name = get_workflow_module_name( module, missing_tool_tups )
+        max_len = len( module_name ) * 1.5
+        text.append( svgfig.Text( x, y + 20, module_name, **{ "font-size": "14px" } ).SVG() )
+        y += 45
+        for di in module_data_inputs:
+            cur_y = y + count * line_px
+            if step.order_index not in in_pos:
+                in_pos[ step.order_index ] = {}
+            in_pos[ step.order_index ][ di[ 'name' ] ] = ( x, cur_y )
+            text.append( svgfig.Text( x, cur_y, di[ 'label' ] ).SVG() )
+            count += 1
+            max_len = max( max_len, len( di[ 'label' ] ) )
+        if len( module.get_data_inputs() ) > 0:
+            y += 15
+        for do in module_data_outputs:
+            cur_y = y + count * line_px
+            if step.order_index not in out_pos:
+                out_pos[ step.order_index ] = {}
+            out_pos[ step.order_index ][ do[ 'name' ] ] = ( x, cur_y )
+            text.append( svgfig.Text( x, cur_y, do[ 'name' ] ).SVG() )
+            count += 1
+            max_len = max( max_len, len( do['name' ] ) )
+        widths[ step.order_index ] = max_len * 5.5
+        max_x = max( max_x, step.position[ 'left' ] )
+        max_y = max( max_y, step.position[ 'top' ] )
+        max_width = max( max_width, widths[ step.order_index ] )
+    for step_dict in data:
+        tool_unavailable = step_dict[ 'tool_errors' ]
+        width = widths[ step_dict[ 'id' ] ]
+        x, y = step_dict[ 'position' ][ 'left' ], step_dict[ 'position' ][ 'top' ]
+        if tool_unavailable:
+            fill = "#EBBCB2"
+        else:
+            fill = "#EBD9B2"    
+        boxes.append( svgfig.Rect( x - margin, y, x + width - margin, y + 30, fill=fill ).SVG() )
+        box_height = ( len( step_dict[ 'data_inputs' ] ) + len( step_dict[ 'data_outputs' ] ) ) * line_px + margin
+        # Draw separator line.
+        if len( step_dict[ 'data_inputs' ] ) > 0:
+            box_height += 15
+            sep_y = y + len( step_dict[ 'data_inputs' ] ) * line_px + 40
+            text.append( svgfig.Line( x - margin, sep_y, x + width - margin, sep_y ).SVG() )
+        # Define an input/output box.
+        boxes.append( svgfig.Rect( x - margin, y + 30, x + width - margin, y + 30 + box_height, fill="#ffffff" ).SVG() )
+        for conn, output_dict in step_dict[ 'input_connections' ].iteritems():
+            in_coords = in_pos[ step_dict[ 'id' ] ][ conn ]
+            # out_pos_index will be a step number like 1, 2, 3...
+            out_pos_index = output_dict[ 'id' ]
+            # out_pos_name will be a string like 'o', 'o2', etc.
+            out_pos_name = output_dict[ 'output_name' ]
+            if out_pos_index in out_pos:
+                # out_conn_index_dict will be something like:
+                # 7: {'o': (824.5, 618)}
+                out_conn_index_dict = out_pos[ out_pos_index ]
+                if out_pos_name in out_conn_index_dict:
+                    out_conn_pos = out_pos[ out_pos_index ][ out_pos_name ]
+                else:
+                    # Take any key / value pair available in out_conn_index_dict.
+                    # A problem will result if the dictionary is empty.
+                    if out_conn_index_dict.keys():
+                        key = out_conn_index_dict.keys()[0]
+                        out_conn_pos = out_pos[ out_pos_index ][ key ]
+            adjusted = ( out_conn_pos[ 0 ] + widths[ output_dict[ 'id' ] ], out_conn_pos[ 1 ] )
+            text.append( svgfig.SVG( "circle",
+                                     cx=out_conn_pos[ 0 ] + widths[ output_dict[ 'id' ] ] - margin,
+                                     cy=out_conn_pos[ 1 ] - margin,
+                                     r = 5,
+                                     fill="#ffffff" ) )
+            connectors.append( svgfig.Line( adjusted[ 0 ],
+                                            adjusted[ 1 ] - margin,
+                                            in_coords[ 0 ] - 10,
+                                            in_coords[ 1 ],
+                                            arrow_end = "true" ).SVG() )
+    canvas.append( connectors )
+    canvas.append( boxes )
+    canvas.append( text )
+    width, height = ( max_x + max_width + 50 ), max_y + 300
+    canvas[ 'width' ] = "%s px" % width
+    canvas[ 'height' ] = "%s px" % height
+    canvas[ 'viewBox' ] = "0 0 %s %s" % ( width, height )
+    trans.response.set_content_type( "image/svg+xml" )
+    return canvas.standalone_xml()
+def get_workflow_data_inputs( step, module ):
+    if module.type == 'tool':
+        if module.tool:
+            return module.get_data_inputs()
+        else:
+            data_inputs = []
+            for wfsc in step.input_connections:
+                data_inputs_dict = {}
+                data_inputs_dict[ 'extensions' ] = [ '' ]
+                data_inputs_dict[ 'name' ] = wfsc.input_name
+                data_inputs_dict[ 'label' ] = 'Unknown'
+                data_inputs.append( data_inputs_dict )
+            return data_inputs
+    return module.get_data_inputs()
+def get_workflow_data_outputs( step, module, steps ):
+    if module.type == 'tool':
+        if module.tool:
+            return module.get_data_outputs()
+        else:
+            data_outputs = []
+            data_outputs_dict = {}
+            data_outputs_dict[ 'extensions' ] = [ 'input' ]
+            found = False
+            for workflow_step in steps:
+                for wfsc in workflow_step.input_connections:
+                    if step.name == wfsc.output_step.name:
+                        data_outputs_dict[ 'name' ] = wfsc.output_name
+                        found = True
+                        break
+                if found:
+                    break
+            if not found:
+                # We're at the last step of the workflow.
+                data_outputs_dict[ 'name' ] = 'output'
+            data_outputs.append( data_outputs_dict )       
+            return data_outputs
+    return module.get_data_outputs()
+def get_workflow_from_dict( trans, workflow_dict, tools_metadata, repository_id, changeset_revision ):
+    """Return a workflow object from the dictionary object created when it was exported."""
+    trans.workflow_building_mode = True
+    workflow = trans.model.Workflow()
+    workflow.name = workflow_dict[ 'name' ]
+    workflow.has_errors = False
+    steps = []
+    # Keep ids for each step that we need to use to make connections.
+    steps_by_external_id = {}
+    # Keep track of tools required by the workflow that are not available in
+    # the tool shed repository.  Each tuple in the list of missing_tool_tups
+    # will be ( tool_id, tool_name, tool_version ).
+    missing_tool_tups = []
+    # First pass to build step objects and populate basic values
+    for key, step_dict in workflow_dict[ 'steps' ].iteritems():
+        # Create the model class for the step
+        step = trans.model.WorkflowStep()
+        step.name = step_dict[ 'name' ]
+        step.position = step_dict[ 'position' ]
+        module = module_factory.from_dict( trans, repository_id, changeset_revision, step_dict, tools_metadata=tools_metadata, secure=False )
+        if module.type == 'tool' and module.tool is None:
+            # A required tool is not available in the current repository.
+            step.tool_errors = 'unavailable'
+            missing_tool_tup = ( step_dict[ 'tool_id' ], step_dict[ 'name' ], step_dict[ 'tool_version' ] )
+            if missing_tool_tup not in missing_tool_tups:
+                missing_tool_tups.append( missing_tool_tup )
+        module.save_to_step( step )
+        if step.tool_errors:
+            workflow.has_errors = True
+        # Stick this in the step temporarily.
+        step.temp_input_connections = step_dict[ 'input_connections' ]
+        steps.append( step )
+        steps_by_external_id[ step_dict[ 'id' ] ] = step
+    # Second pass to deal with connections between steps.
+    for step in steps:
+        # Input connections.
+        for input_name, conn_dict in step.temp_input_connections.iteritems():
+            if conn_dict:
+                output_step = steps_by_external_id[ conn_dict[ 'id' ] ]
+                conn = trans.model.WorkflowStepConnection()
+                conn.input_step = step
+                conn.input_name = input_name
+                conn.output_step = output_step
+                conn.output_name = conn_dict[ 'output_name' ]
+                step.input_connections.append( conn )
+        del step.temp_input_connections
+    # Order the steps if possible.
+    galaxy.webapps.galaxy.controllers.workflow.attach_ordered_steps( workflow, steps )
+    return workflow, missing_tool_tups
+def get_workflow_module_name( module, missing_tool_tups ):
+    module_name = module.get_name()
+    if module.type == 'tool' and module_name == 'unavailable':
+        for missing_tool_tup in missing_tool_tups:
+            missing_tool_id, missing_tool_name, missing_tool_version = missing_tool_tup
+            if missing_tool_id == module.tool_id:
+                module_name = '%s' % missing_tool_name
+                break
+    return module_name
\ No newline at end of file


diff -r 875ac898df00fd919b6b24f58562fadbf03dc5e1 -r 7073d786cad0f0d251d4ea9b2c42171f698cf953 lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
--- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
+++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
@@ -1,10 +1,10 @@
 import urllib2, tempfile
 from admin import *
-from galaxy.util.json import from_json_string, to_json_string
+from galaxy.util import json
 import galaxy.util.shed_util as shed_util
 import galaxy.util.shed_util_common as suc
 from galaxy.tool_shed import encoding_util
-from galaxy.webapps.community.util import container_util
+from galaxy.webapps.community.util import container_util, workflow_util
 from galaxy import eggs, tools
 
 eggs.require( 'mercurial' )
@@ -552,6 +552,11 @@
         galaxy_url = url_for( '/', qualified=True )
         url = suc.url_join( tool_shed_url, 'repository/find_workflows?galaxy_url=%s' % galaxy_url )
         return trans.response.send_redirect( url )
+    @web.expose
+    @web.require_admin
+    def generate_workflow_image( self, trans, workflow_name, repository_id=None ):
+        """Return an svg image representation of a workflow dictionary created when the workflow was exported."""
+        return workflow_util.generate_workflow_image( trans, workflow_name, repository_metadata_id=None, repository_id=repository_id )
     @web.json
     @web.require_admin
     def get_file_contents( self, trans, file_path ):
@@ -576,7 +581,7 @@
         raw_text = response.read()
         response.close()
         if len( raw_text ) > 2:
-            encoded_text = from_json_string( raw_text )
+            encoded_text = json.from_json_string( raw_text )
             text = encoding_util.tool_shed_decode( encoded_text )
         else:
             text = ''
@@ -586,6 +591,71 @@
         return tool_version.get_version_ids( app, reverse=True )
     @web.expose
     @web.require_admin
+    def import_workflow( self, trans, workflow_name, repository_id, **kwd ):
+        # FIXME: importing doesn't yet work...
+        params = util.Params( kwd )
+        message = util.restore_text( params.get( 'message', ''  ) )
+        status = params.get( 'status', 'done' )
+        if workflow_name:
+            workflow_name = encoding_util.tool_shed_decode( workflow_name )
+        repository = suc.get_tool_shed_repository_by_id( trans, repository_id )
+        changeset_revision = repository.changeset_revision
+        metadata = repository.metadata
+        workflows = metadata[ 'workflows' ]
+        tools_metadata = metadata[ 'tools' ]
+        workflow_dict = None
+        for workflow_data_tuple in workflows:
+            # The value of workflow_data_tuple is ( relative_path_to_workflow_file, exported_workflow_dict ).
+            relative_path_to_workflow_file, exported_workflow_dict = workflow_data_tuple
+            if exported_workflow_dict[ 'name' ] == workflow_name:
+                # If the exported workflow is available on disk, import it.
+                if os.path.exists( relative_path_to_workflow_file ):
+                    workflow_file = open( relative_path_to_workflow_file, 'rb' )
+                    workflow_data = workflow_file.read()
+                    workflow_file.close()
+                    workflow_dict = json.from_json_string( workflow_data )
+                else:
+                    # Use the current exported_workflow_dict.
+                    workflow_dict = exported_workflow_dict
+                break
+        if workflow_dict:
+            # Create workflow if possible.  If a required tool is not available in the local
+            # Galaxy instance, the tool information will be available in the step_dict.
+            src = None
+            workflow, missing_tool_tups = workflow_util.get_workflow_from_dict( trans,
+                                                                                workflow_dict,
+                                                                                tools_metadata,
+                                                                                repository_id,
+                                                                                changeset_revision )
+            if workflow_name:
+                workflow.name = workflow_name
+            # Provide user feedback and show workflow list.
+            if workflow.has_errors:
+                message += "Imported, but some steps in this workflow have validation errors. "
+                status = "error"
+            if workflow.has_cycles:
+                message += "Imported, but this workflow contains cycles.  "
+                status = "error"
+            else:
+                message += "Workflow <b>%s</b> imported successfully.  " % workflow.name
+            if missing_tool_tups:
+                # TODO: rework this since it is used in the tool shed, but shoudn't be used in Galaxy.
+                name_and_id_str = ''
+                for missing_tool_tup in missing_tool_tups:
+                    tool_id, tool_name, other = missing_tool_tup
+                    name_and_id_str += 'name: %s, id: %s' % ( str( tool_id ), str( tool_name ) )
+                log.debug( "The following tools required by this workflow are missing from this Galaxy instance: %s" % name_and_id_str )
+        else:
+            message += 'The workflow named %s is not included in the metadata for revision %s of repository %s' % \
+                ( str( workflow_name ), str( changeset_revision ), str( repository.name ) )
+            status = 'error'
+        return trans.response.send_redirect( web.url_for( controller='admin_toolshed',
+                                                          action='browse_repository',
+                                                          id=repository_id,
+                                                          message=message,
+                                                          status=status ) )
+    @web.expose
+    @web.require_admin
     def initiate_repository_installation( self, trans, shed_repository_ids, encoded_kwd, reinstalling=False ):
         tsr_ids = util.listify( shed_repository_ids )
         tool_shed_repositories = []
@@ -728,7 +798,7 @@
                     text = response.read()
                     response.close()
                     if text:
-                        tool_version_dicts = from_json_string( text )
+                        tool_version_dicts = json.from_json_string( text )
                         shed_util.handle_tool_versions( trans.app, tool_version_dicts, tool_shed_repository )
                     else:
                         message += "Version information for the tools included in the <b>%s</b> repository is missing.  " % name
@@ -1084,7 +1154,7 @@
             response = urllib2.urlopen( url )
             raw_text = response.read()
             response.close()
-            repo_information_dict = from_json_string( raw_text )
+            repo_information_dict = json.from_json_string( raw_text )
             includes_tools = util.string_as_bool( repo_information_dict.get( 'includes_tools', False ) )
             includes_repository_dependencies = util.string_as_bool( repo_information_dict.get( 'includes_repository_dependencies', False ) )
             includes_tool_dependencies = util.string_as_bool( repo_information_dict.get( 'includes_tool_dependencies', False ) )
@@ -1191,7 +1261,7 @@
             response = urllib2.urlopen( url )
             raw_text = response.read()
             response.close()
-            readme_files_dict = from_json_string( raw_text )
+            readme_files_dict = json.from_json_string( raw_text )
             # Since we are installing a new repository, no tool dependencies will be considered "missing".  Most of the repository contents
             # are set to None since we don't yet know what they are.
             containers_dict = suc.build_repository_containers_for_galaxy( trans=trans,
@@ -1593,7 +1663,7 @@
         text = response.read()
         response.close()
         if text:
-            tool_version_dicts = from_json_string( text )
+            tool_version_dicts = json.from_json_string( text )
             shed_util.handle_tool_versions( trans.app, tool_version_dicts, repository )
             message = "Tool versions have been set for all included tools."
             status = 'done'
@@ -1785,7 +1855,26 @@
                                     tool_lineage=tool_lineage,
                                     message=message,
                                     status=status )
-
+    @web.expose
+    @web.require_admin
+    def view_workflow( self, trans, workflow_name=None, repository_id=None, **kwd ):
+        """Retrieve necessary information about a workflow from the database so that it can be displayed in an svg image."""
+        params = util.Params( kwd )
+        message = util.restore_text( params.get( 'message', ''  ) )
+        status = params.get( 'status', 'done' )
+        if workflow_name:
+            workflow_name = encoding_util.tool_shed_decode( workflow_name )
+        repository = suc.get_tool_shed_repository_by_id( trans, repository_id )
+        changeset_revision = repository.changeset_revision
+        metadata = repository.metadata
+        return trans.fill_template( "/admin/tool_shed_repository/view_workflow.mako",
+                                    repository=repository,
+                                    changeset_revision=changeset_revision,
+                                    repository_id=repository_id,
+                                    workflow_name=workflow_name,
+                                    metadata=metadata,
+                                    message=message,
+                                    status=status )
 ## ---- Utility methods -------------------------------------------------------
 
 def build_shed_tool_conf_select_field( trans ):


diff -r 875ac898df00fd919b6b24f58562fadbf03dc5e1 -r 7073d786cad0f0d251d4ea9b2c42171f698cf953 lib/galaxy/workflow/modules.py
--- a/lib/galaxy/workflow/modules.py
+++ b/lib/galaxy/workflow/modules.py
@@ -2,7 +2,7 @@
 from elementtree.ElementTree import Element
 from galaxy import web
 from galaxy.tools.parameters import DataToolParameter, DummyDataset, RuntimeValue, check_param, visit_input_values
-from galaxy.tools import DefaultToolState
+import galaxy.tools
 from galaxy.util.bunch import Bunch
 from galaxy.util.json import from_json_string, to_json_string
 from galaxy.jobs.actions.post import ActionBox
@@ -139,7 +139,7 @@
         return dict( input=DataToolParameter( None, Element( "param", name="input", label=label, multiple=True, type="data", format=', '.join(filter_set) ), self.trans ) )
 
     def get_runtime_state( self ):
-        state = DefaultToolState()
+        state = galaxy.tools.DefaultToolState()
         state.inputs = dict( input=None )
         return state
 
@@ -149,7 +149,7 @@
 
     def decode_runtime_state( self, trans, string ):
         fake_tool = Bunch( inputs = self.get_runtime_inputs() )
-        state = DefaultToolState()
+        state = galaxy.tools.DefaultToolState()
         state.decode( string, fake_tool, trans.app )
         return state
 
@@ -192,7 +192,7 @@
     def from_dict( Class, trans, d, secure=True ):
         tool_id = d[ 'tool_id' ]
         module = Class( trans, tool_id )
-        module.state = DefaultToolState()
+        module.state = galaxy.tools.DefaultToolState()
         if module.tool is not None:
             module.state.decode( d[ "tool_state" ], module.tool, module.trans.app, secure=secure )
         module.errors = d.get( "tool_errors", None )
@@ -213,7 +213,7 @@
                 tool_id = tool.id
         if ( trans.app.toolbox and tool_id in trans.app.toolbox.tools_by_id ):
             module = Class( trans, tool_id )
-            module.state = DefaultToolState()
+            module.state = galaxy.tools.DefaultToolState()
             module.state.inputs = module.tool.params_from_strings( step.tool_inputs, trans.app, ignore_errors=True )
             module.errors = step.tool_errors
             # module.post_job_actions = step.post_job_actions


diff -r 875ac898df00fd919b6b24f58562fadbf03dc5e1 -r 7073d786cad0f0d251d4ea9b2c42171f698cf953 templates/admin/tool_shed_repository/view_workflow.mako
--- /dev/null
+++ b/templates/admin/tool_shed_repository/view_workflow.mako
@@ -0,0 +1,45 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+<%namespace file="/webapps/community/common/common.mako" import="*" />
+<%namespace file="/webapps/community/repository/common.mako" import="*" />
+
+<%
+    from galaxy.web.framework.helpers import time_ago
+    from galaxy.tool_shed.encoding_util import tool_shed_encode
+%>
+
+<%!
+   def inherit(context):
+       if context.get('use_panels'):
+           return '/webapps/community/base_panels.mako'
+       else:
+           return '/base.mako'
+%>
+<%inherit file="${inherit(context)}"/>
+
+<%def name="render_workflow( workflow_name, repository_id )">
+    <% center_url = h.url_for( controller='admin_toolshed', action='generate_workflow_image', workflow_name=tool_shed_encode( workflow_name ), repository_id=repository_id ) %>
+    <iframe name="galaxy_main" id="galaxy_main" frameborder="0" style="position: absolute; width: 100%; height: 100%;" src="${center_url}"></iframe>
+</%def>
+
+<br/><br/>
+<ul class="manage-table-actions">
+    <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li>
+    <div popupmenu="repository-${repository.id}-popup">
+        <li><a class="action-button" href="${h.url_for( controller='admin_toolshed', action='import_workflow', workflow_name=tool_shed_encode( workflow_name ), repository_id=repository_id )}">Import workflow to Galaxy</a></li>
+    </div>
+</ul>
+
+%if message:
+    ${render_msg( message, status )}
+%endif
+
+<div class="toolFormTitle">${workflow_name | h}</div>
+<div class="form-row">
+    <div class="toolParamHelp" style="clear: both;">
+        (this page displays SVG graphics)
+    </div>
+</div>
+<br clear="left"/>
+
+${render_workflow( workflow_name, repository_id )}


diff -r 875ac898df00fd919b6b24f58562fadbf03dc5e1 -r 7073d786cad0f0d251d4ea9b2c42171f698cf953 templates/webapps/community/repository/common.mako
--- a/templates/webapps/community/repository/common.mako
+++ b/templates/webapps/community/repository/common.mako
@@ -231,6 +231,10 @@
                         folder_label = "%s<i> - this repository's tools require handling of these dependencies</i>" % folder_label
                     col_span_str = 'colspan="4"'
                 elif folder.workflows:
+                    if folder.description:
+                        folder_label = "%s<i> - %s</i>" % ( folder_label, folder.description )
+                    else:
+                        folder_label = "%s<i> - click the name to view an SVG image of the workflow</i>" % folder_label
                     col_span_str = 'colspan="4"'
             %><td ${col_span_str} style="padding-left: ${folder_pad}px;">
@@ -439,7 +443,11 @@
                             <a class="action-button" href="${h.url_for( controller='repository', action='view_tool_metadata', repository_id=trans.security.encode_id( tool.repository_id ), changeset_revision=tool.changeset_revision, tool_id=tool.tool_id )}">View tool metadata</a></div>
                     %else:
-                        <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='view_tool_metadata', repository_id=trans.security.encode_id( tool.repository_id ), changeset_revision=tool.changeset_revision, tool_id=tool.tool_id )}">${tool.name | h}</a>
+                        %if tool.repository_installation_status == trans.model.ToolShedRepository.installation_status.INSTALLED:
+                            <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='view_tool_metadata', repository_id=trans.security.encode_id( tool.repository_id ), changeset_revision=tool.changeset_revision, tool_id=tool.tool_id )}">${tool.name | h}</a>
+                        %else:
+                            ${tool.name | h}
+                        %endif
                     %endif
                 %else:
                     ${tool.name | h}
@@ -515,6 +523,13 @@
     <%
         from galaxy.tool_shed.encoding_util import tool_shed_encode
         encoded_id = trans.security.encode_id( workflow.id )
+        encoded_workflow_name = tool_shed_encode( workflow.workflow_name )
+        if trans.webapp.name == 'community':
+            encoded_repository_metadata_id = trans.security.encode_id( workflow.repository_metadata_id )
+            encoded_repository_id = None
+        else:
+            encoded_repository_metadata_id = None
+            encoded_repository_id = trans.security.encode_id( workflow.repository_id )
         if row_is_header:
             cell_type = 'th'
         else:
@@ -528,8 +543,12 @@
         <${cell_type} style="padding-left: ${pad+20}px;">
             %if row_is_header:
                 ${workflow.workflow_name | h}
+            %elif trans.webapp.name == 'community' and encoded_repository_metadata_id:
+                <a href="${h.url_for( controller='repository', action='view_workflow', workflow_name=encoded_workflow_name, repository_metadata_id=encoded_repository_metadata_id )}">${workflow.workflow_name | h}</a>
+            %elif trans.webapp.name == 'galaxy' and encoded_repository_id:
+                <a href="${h.url_for( controller='admin_toolshed', action='view_workflow', workflow_name=encoded_workflow_name, repository_id=encoded_repository_id )}">${workflow.workflow_name | h}</a>
             %else:
-                <a href="${h.url_for( controller='workflow', action='view_workflow', repository_metadata_id=trans.security.encode_id( workflow.repository_metadata_id ), workflow_name=tool_shed_encode( workflow.workflow_name ) )}">${workflow.workflow_name | h}</a>
+                ${workflow.workflow_name | h}
             %endif
         </${cell_type}><${cell_type}>${workflow.steps | h}</${cell_type}>
@@ -557,7 +576,7 @@
         missing_repository_dependencies_root_folder = containers_dict.get( 'missing_repository_dependencies', None )
         tool_dependencies_root_folder = containers_dict.get( 'tool_dependencies', None )
         missing_tool_dependencies_root_folder = containers_dict.get( 'missing_tool_dependencies', None )
-        valid_tools_root_folder = containers_dict.get( 'valid_tools', none )
+        valid_tools_root_folder = containers_dict.get( 'valid_tools', None )
         workflows_root_folder = containers_dict.get( 'workflows', None )
         
         has_contents = datatypes_root_folder or invalid_tools_root_folder or valid_tools_root_folder or workflows_root_folder


diff -r 875ac898df00fd919b6b24f58562fadbf03dc5e1 -r 7073d786cad0f0d251d4ea9b2c42171f698cf953 templates/webapps/community/repository/view_workflow.mako
--- a/templates/webapps/community/repository/view_workflow.mako
+++ b/templates/webapps/community/repository/view_workflow.mako
@@ -7,22 +7,23 @@
     from galaxy.web.framework.helpers import time_ago
     from galaxy.tool_shed.encoding_util import tool_shed_encode
 
-    in_tool_shed = trans.webapp.name == 'community'
     is_admin = trans.user_is_admin()
     is_new = repository.is_new( trans.app )
     can_manage = is_admin or trans.user == repository.user
-    can_contact_owner = in_tool_shed and trans.user and trans.user != repository.user
-    can_push = in_tool_shed and trans.app.security_agent.can_push( trans.app, trans.user, repository )
+    can_contact_owner = trans.user and trans.user != repository.user
+    can_push = trans.app.security_agent.can_push( trans.app, trans.user, repository )
     can_upload = can_push
-    can_download = in_tool_shed and not is_new and ( not is_malicious or can_push )
-    can_browse_contents = in_tool_shed and not is_new
-    can_rate = in_tool_shed and not is_new and trans.user and repository.user != trans.user
-    can_view_change_log = in_tool_shed and not is_new
+    can_download = not is_new and ( not is_malicious or can_push )
+    can_browse_contents = not is_new
+    can_rate = not is_new and trans.user and repository.user != trans.user
+    can_view_change_log = not is_new
     if can_push:
         browse_label = 'Browse or delete repository tip files'
     else:
         browse_label = 'Browse repository tip files'
-    has_readme = metadata and 'readme' in metadata
+    has_readme = metadata and 'readme_files' in metadata
+    
+    # <li><a class="action-button" href="${h.url_for( controller='repository', action='install_repositories_by_revision', repository_ids=trans.security.encode_id( repository.id ), changeset_revisions=changeset_revision )}">Install repository to Galaxy</a></li>
 %><%!
@@ -34,57 +35,43 @@
 %><%inherit file="${inherit(context)}"/>
 
-<%def name="render_workflow( repository_metadata_id, workflow_name )">
-    <% center_url = h.url_for( controller='workflow', action='generate_workflow_image', repository_metadata_id=repository_metadata_id, workflow_name=tool_shed_encode( workflow_name ) ) %>
+<%def name="render_workflow( workflow_name, repository_metadata_id )">
+    <% center_url = h.url_for( controller='repository', action='generate_workflow_image', workflow_name=tool_shed_encode( workflow_name ), repository_metadata_id=repository_metadata_id, repository_id=None ) %><iframe name="galaxy_main" id="galaxy_main" frameborder="0" style="position: absolute; width: 100%; height: 100%;" src="${center_url}"></iframe></%def><br/><br/><ul class="manage-table-actions">
-    %if in_tool_shed:
-        %if is_new and can_upload:
-            <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}">Upload files to repository</a>
-        %else:
-            <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li>
-            <div popupmenu="repository-${repository.id}-popup">
-                %if can_upload:
-                    <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}">Upload files to repository</a>
-                %endif
-                %if can_manage:
-                    <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip( trans.app ) )}">Manage repository</a>
-                %else:
-                    <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip( trans.app ) )}">View repository</a>
-                %endif
-                %if can_view_change_log:
-                    <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">View change log</a>
-                %endif
-                %if can_rate:
-                    <a class="action-button" href="${h.url_for( controller='repository', action='rate_repository', id=trans.app.security.encode_id( repository.id ) )}">Rate repository</a>
-                %endif
-                %if can_browse_contents:
-                    <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">${browse_label}</a>
-                %endif
-                %if can_contact_owner:
-                    <a class="action-button" href="${h.url_for( controller='repository', action='contact_owner', id=trans.security.encode_id( repository.id ) )}">Contact repository owner</a>
-                %endif
-                %if can_download:
-                    <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='gz' )}">Download as a .tar.gz file</a>
-                    <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='bz2' )}">Download as a .tar.bz2 file</a>
-                    <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='zip' )}">Download as a zip file</a>
-                %endif
-            </div>
-        %endif
+    %if is_new and can_upload:
+        <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}">Upload files to repository</a>
     %else:
         <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li><div popupmenu="repository-${repository.id}-popup">
-            <li><a class="action-button" href="${h.url_for( controller='workflow', action='import_workflow', repository_metadata_id=repository_metadata_id, workflow_name=tool_shed_encode( workflow_name ) )}">Import workflow to local Galaxy</a></li>
-            <li><a class="action-button" href="${h.url_for( controller='repository', action='install_repositories_by_revision', repository_ids=trans.security.encode_id( repository.id ), changeset_revisions=changeset_revision )}">Install repository to local Galaxy</a></li>
-        </div>
-        <li><a class="action-button" id="toolshed-${repository.id}-popup" class="menubutton">Tool Shed Actions</a></li>
-        <div popupmenu="toolshed-${repository.id}-popup">
-            <a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_categories' )}">Browse valid repositories</a>
-            <a class="action-button" href="${h.url_for( controller='repository', action='find_tools' )}">Search for valid tools</a>
-            <a class="action-button" href="${h.url_for( controller='repository', action='find_workflows' )}">Search for workflows</a>
+            %if can_upload:
+                <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}">Upload files to repository</a>
+            %endif
+            %if can_manage:
+                <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip( trans.app ) )}">Manage repository</a>
+            %else:
+                <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip( trans.app ) )}">View repository</a>
+            %endif
+            %if can_view_change_log:
+                <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">View change log</a>
+            %endif
+            %if can_rate:
+                <a class="action-button" href="${h.url_for( controller='repository', action='rate_repository', id=trans.app.security.encode_id( repository.id ) )}">Rate repository</a>
+            %endif
+            %if can_browse_contents:
+                <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">${browse_label}</a>
+            %endif
+            %if can_contact_owner:
+                <a class="action-button" href="${h.url_for( controller='repository', action='contact_owner', id=trans.security.encode_id( repository.id ) )}">Contact repository owner</a>
+            %endif
+            %if can_download:
+                <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='gz' )}">Download as a .tar.gz file</a>
+                <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='bz2' )}">Download as a .tar.bz2 file</a>
+                <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='zip' )}">Download as a zip file</a>
+            %endif
         </div>
     %endif
 </ul>
@@ -102,4 +89,4 @@
 </div><br clear="left"/>
 
-${render_workflow( repository_metadata_id, workflow_name )}
+${render_workflow( workflow_name, repository_metadata_id )}


diff -r 875ac898df00fd919b6b24f58562fadbf03dc5e1 -r 7073d786cad0f0d251d4ea9b2c42171f698cf953 test/tool_shed/base/twilltestcase.py
--- a/test/tool_shed/base/twilltestcase.py
+++ b/test/tool_shed/base/twilltestcase.py
@@ -454,9 +454,11 @@
               ( self.security.encode_id( repository.id ), tool_xml_path, changeset_revision )
         self.visit_url( url )
         self.check_for_strings( strings_displayed, strings_not_displayed )
-    def load_workflow_image( self, repository, workflow_name, strings_displayed=[], strings_not_displayed=[] ):
+    def load_workflow_image_in_tool_shed( self, repository, workflow_name, strings_displayed=[], strings_not_displayed=[] ):
+        # FIXME: Can not always assume the first repository_metadata record is the correct one.
+        # TODO: Add a method for displaying a workflow image in Galaxy.
         metadata = self.get_repository_metadata( repository )
-        url = '/workflow/generate_workflow_image?repository_metadata_id=%s&workflow_name=%s' % \
+        url = '/repository/generate_workflow_image?repository_metadata_id=%s&workflow_name=%s' % \
               ( self.security.encode_id( metadata[0].id ), tool_shed_encode( workflow_name ) )
         self.visit_url( url )
         self.check_for_strings( strings_displayed, strings_not_displayed )


diff -r 875ac898df00fd919b6b24f58562fadbf03dc5e1 -r 7073d786cad0f0d251d4ea9b2c42171f698cf953 test/tool_shed/functional/test_0060_workflows.py
--- a/test/tool_shed/functional/test_0060_workflows.py
+++ b/test/tool_shed/functional/test_0060_workflows.py
@@ -46,7 +46,7 @@
                           workflow_filename, 
                           filepath=workflow_filepath, 
                           commit_message='Uploaded filtering workflow.' )
-        self.load_workflow_image( repository, workflow_name, strings_displayed=[ '#EBBCB2' ] )
+        self.load_workflow_image_in_tool_shed( repository, workflow_name, strings_displayed=[ '#EBBCB2' ] )
     def test_0020_upload_tool( self ):
         '''Upload the missing tool for the workflow in the previous step, and verify that the error is no longer present.'''
         repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name )
@@ -54,7 +54,7 @@
                           'filtering/filtering_2.2.0.tar', 
                           commit_message="Uploaded filtering 2.2.0", 
                           remove_repo_files_not_in_tar='No' )
-        self.load_workflow_image( repository, workflow_name, strings_not_displayed=[ '#EBBCB2' ] )
+        self.load_workflow_image_in_tool_shed( repository, workflow_name, strings_not_displayed=[ '#EBBCB2' ] )
     def test_0025_verify_repository_metadata( self ):
         '''Verify that resetting the metadata does not change it.'''
         repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name )

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